Schizophrenia methods and compositions

ABSTRACT

Methods of preparing and using neural cells derived from human induced pluripotent stem cell (hiPSCs), particularly hiPSCs derived from subjects with schizophrenia are provided. The hiPSC-derived neural cells can be used to screen test compounds and to identify schizophrenia marker functions. The hiPSC-derived neural cells can be used to diagnose and/or assess the severity of schizophrenia in a subject. Further, may the hiPSC-derived neural cells from a subject be used as an in vitro system to identify the most effective candidate among existing drugs for that specific subject (i.e. personalized medicine).

CROSS-REFERENCES TO RELATED APPLICATIONS

This application claims the benefit of U.S. Provisional Application No. 61/414,380 filed Nov. 16, 2010, which is hereby incorporated in its entirety and for all purposes.

REFERENCE TO A “SEQUENCE LISTING,” A TABLE, OR A COMPUTER PROGRAM LISTING APPENDIX SUBMITTED AS AN ASCII FILE

The Sequence Listing written in file 92150-824615_ST25.TXT, created on Nov. 8, 2011, 17,990 bytes, machine format IBM-PC, MS-Windows operating system, is hereby incorporated by reference in its entirety and for all purposes.

BACKGROUND OF THE INVENTION

Schizophrenia is now believed to be a developmental disorder with late manifestation of its characteristic symptoms. Onset is typically in adolescence or early adulthood, occasionally in childhood. 1.1% of the population over the age of 18 suffers from schizophrenia. See Association, A. P. Diagnostic and statistical manual of mental disorders: DSM-IV. 3rd ed., Rev. Edn., Vol. 4th ed., American Psychiatric Press, 1994. Schizophrenia often results in premature death from poverty, homelessness, substance abuse and poor health maintenance (Brown, S., Inskip, H. & Barraclough, B., 2000, Br J Psychiatry 177:212-217); the life expectancy of schizophrenic patients is up to ten years less than the general population (Hannerz, H., Borga, P. & Borritz, M., 2001, Public Health 115:328-337).

There is a strong genetic component to schizophrenia, with an estimated heritability of 80-85% (Cardno, A. G. & Gottesman, I I., 2000, Am J Med. Genet. 97:12-17; Sullivan, P. F., Kendler, K. S. & Neale, M. C., 2003, Arch Gen Psychiatry 60:1187-1192). Single nucleotide polymorphisms (SNPs), common polygenic variation involving thousands of alleles of very small effect, account for nearly 30% of the genetic variance of schizophrenia (Shi, J. et al., 2009, Nature 460:753-757; Stefansson, H. et al., 2009, Nature 460:744-747; Purcell, S. M. et al., 2009, Nature 460:748-752). Copy number variants (CNVs), rare structural disruptions of genes, such as ERBB4 (Walsh, T. et al., 2008, Science 320:539-543) or NRXN1 (Kirov, G. et al., 2008, Human Molecular Genetics 17:458-465), or regions, including 1q21.1, 15q11.2, 15q13.3, 16p11.2, 22q11.2 (Walsh, T. et al., 2008, Science 320:539-543; Mefford, H. C. et al., 2008, The New England Journal of Medicine 359:1685-1699; Stefansson, H. et al., 2008, Nature 455:232-236; Nature 455:237-241 (2008)), are highly penetrant but account for only 20% of cases. Numerous disruptions in any number of key neurodevelopmental pathways may be sufficient to produce a diseased state that could ultimately manifest as schizophrenia.

Postmortem studies of schizophrenic brain tissue have observed reduced volume (Bogerts, B. et al., 1990, Schizophr Res. 3:295-301), cell size (Zaidel, D. W., Esiri, M. M. & Harrison, 1997, P. J., Am J Psychiatry 154:812-818 (1997), spine density (Glantz, L. A. & Lewis, D. A., 2000, Arch Gen Psychiatry 57:65-73; Hill, J. J., Hashimoto, T. & Lewis, D. A., 2006, Molecular psychiatry 11:557-566 (2006)) and pyramidal cell disarray (Jonsson, S. A et al., 1997, Eur Arch Psychiatry Clin Neurosci. 247:120-127 (1997); Conrad, A. J. et al., 1991, Arch Gen Psychiatry 48:413-417) in the hippocampus and reduced cortical thickness (Selemon, L. D., Rajkowska, G. & Goldman-Rakic, P., 1998, J Comp Neurol. 392:402-412), cell size (Pierri, J. N. et al., 2003, Biol Psychiatry 54:111-120) and abnormal neural distribution (Vogeley, K. et al., 2000, Am J Psychiatry 157:34-39) in the prefrontal cortex. Neuropharmacological studies have implicated dopaminergic, glutamatergic and GABAergic activity in schizophrenia (Javitt, D. C. et al., Nat Rev Drug Discov. 7:68-83). The cell type affected in schizophrenia and the molecular mechanisms underlying the disease state remains unclear.

There is a need in the art for methods of directly reprogramming fibroblasts from schizophrenic patients into hiPSCs and subsequently differentiating these disorder-specific hiPSCs into neurons as well as cell-based models permitting the characterization of complex genetic psychiatric diseases using hiPSCs. Provided herein are solutions to these and other needs in the art, by, inter alia, identifying neural phenotypes and gene expression changes associated with schizophrenic neurons in vitro, advancing the field of hiPSC-based disease modeling and developing a transformative new tool with which to study schizophrenia.

BRIEF SUMMARY OF THE INVENTION

Provided herein are, inter alia, methods of preparing and using neural cells derived from human induced pluripotent stem cell (hiPSCs), particularly hiPSCs derived from subjects with schizophrenia. The hiPSC-derived neural cells can be used to screen test compounds and to identify schizophrenia marker functions. By creating hiPSC-derived neural cells from a subject, one can use the hiPSC-derived neural cells to diagnose and/or assess the severity of schizophrenia in that subject. Further, may the hiPSC-derived neural cells from a subject be used as an in vitro system to identify the most effective candidate among existing drugs for that specific subject (i.e. personalized medicine).

In one aspect, a method of determining whether a test compound is capable of improving a schizophrenia marker function in a hiPSC-derived neural cell is provided. The method includes contacting a test compound with a hiPSC-derived neural cell derived from a schizophrenic subject. The hiPSC-derived neural cell exhibits a schizophrenia marker function at a first level in the absence of the test compound. Then, a second level of the schizophrenia marker function is determined in the presence of the test compound. The second level is compared to a control level. A smaller difference between the second level and the control level than between the first level and the control level indicates that the test compound is capable of improving the schizophrenia marker function.

In another aspect, a method of determining whether a subject is schizophrenic is provided. The method includes determining a level of a schizophrenia marker function in a hiPSC-derived neural cell derived from a subject and comparing the level to a control level. A difference between the determined level and the control level indicates that the subject is schizophrenic.

In another aspect, a method of identifying a schizophrenia marker function is provided. The method includes obtaining a cell from a schizophrenic subject and reprogramming the cell thereby forming a hiPSC. The hiPSC is allowed to differentiate thereby forming a hiPSC-derived neural cell derived from the schizophrenic subject. A level of a function of the hiPSC-derived neural cell is determined and the level is compared to a control level. A difference between the level and the control level indicates the function is a schizophrenia marker function.

In one aspect, a method of determining whether a schizophrenic subject is responsive to treatment with a loxapine compound is provided. The method includes contacting a loxapine compound with a hiPSC-derived neural cell. The hiPSC-derived neural cell is derived from the schizophrenic subject, and the hiPSC-derived neural cell exhibits a loxapine marker function at a first level in the absence of a loxapine compound. Then a second level of the loxapine marker function is determined and the second level is compared to a control level. A smaller difference between the second level and the control level than between the first level and the control level indicates the schizophrenic subject is responsive to treatment with a loxapine compound.

In another aspect, a method of determining whether a test compound is capable of improving a loxapine marker function is provided. The method includes contacting a test compound with a hiPSC-derived neural cell. The hiPSC-derived neural cell is derived from a schizophrenic subject, and the hiPSC-derived neural cell exhibits a loxapine marker function at a first level in the absence of the test compound. Then a second level of the loxapine marker function determined and the second level is compared to a control level. A smaller difference between the second level and the control level than between the first level and the control level indicates the test compound is capable of improving the loxapine marker function.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1. Patient-specific hiPSCs, NPCs and neurons. Left panel FIG. 1: hiPSCs express NANOG and TRA-1-60. DAPI. ×100, scale bar 100 μm. Centre panel FIG. 1: hiPSC neural progenitor cells (NPCs) express NESTIN and SOX2 and DAPI. ×600, scale bar 100 μm. Right panel FIG. 1: hiPSC neurons express βIII-tubulin and the dendritic marker MAP2AB and DAPI. ×200, scale bar 100 μm.

FIG. 2. Decreased neural connectivity in schizophrenic hiPSC-derived neurons. FIG. 2A. Representative images of control and SCZD hiPSC neurons cotransduced with LV-SYNP-HTG and Rabies-ENVAΔG-RFP, 10 days post rabies transduction. All images were captured using identical laser power and gain settings. βIII-tubulin staining of the field is shown below each panel. ×400, scale bar 80 μm. FIG. 2B. Histogram showing treatment of SCZD hiPSC neurons with Loxapine resulted in a statistically significant improvement in neuronal connectivity. Error bars are s.e. (standard error), *P<0.05

FIG. 3. Decreased neurites and synaptic density but normal calcium transient activity in schizophrenic hiPSC-derived neurons. FIG. 3A: Histogram showing decreased neurites in SCZD hiPSC neurons. FIG. 3B. Histogram showing decreased PSD95 protein relative to MAP2AB for SCZD hiPSC neurons. FIG. 3C. Histogram showing a trend of decreased PSD95 synaptic density in SCZD hiPSC neurons. FIG. 3D-G. Electrophysiological characterization. hiPSC neurons cultured on astrocytes show normal sodium and potassium currents when voltage-clamped (FIG. 3D), normal induced action potentials when current-clamped (FIG. 3E), and spontaneous excitatory (FIG. 3F) and inhibitory (FIG. 3G) synaptic activity. FIG. 3H-K. Spontaneous calcium transient imaging. Representative spontaneous Fluo-4AM calcium traces of fluorescent intensity versus time generated from three-month-old hiPSC neurons (FIG. 3H). Histogram showing no difference between the spike amplitude of spontaneous calcium transients of control and SCZD hiPSC neurons (FIG. 3I). Histogram showing no difference between the total numbers of spontaneous calcium transients per total number of ROIs in cultures of control and SCZD hiPSC neurons (FIG. 3J). Histogram showing no change in percentage synchronicity per calcium transient in control and SCZD hiPSC neurons (FIG. 3K). Error bars are SE. Asterisks used as follows: *** p<0.001.

FIG. 4. RNA expression analysis of control and schizophrenic hiPS-derived neurons. Heat maps showing microarray expression profiles of altered expression of glutamate receptors (FIG. 4A), cAMP signaling (FIG. 4B), and WNT signaling (FIG. 4C) genes in SCZD hiPSC neurons. Fold-change and p-values (diagnosis) provided to the right of each heat map. FIG. 4D. Heat maps showing perturbed expression of NRG1 and ANK3 in all four SCZD patients, as well as altered expression of ZNF804A, GABRB1, ERBB4, DISC1 and PDE4B in some but not all patients. Fold-change and p-values (diagnosis) provided to the right of each heat map. FIG. 4E. Altered expression of NRG1 is detected in SCZD hiPSC neurons but not in patient fibroblasts, hiPSCs or hiPSC NPCs. FIG. 4F. qPCR validation of altered expression of NRG1, GRIK1, ADCY8, PRKCA, WNT7A, TCF4 and DISC1, as well as response to three weeks of treatment with Loxapine (striped bars) in six-week-old hiPSC neurons. Asterisks used as follows: * p<0.05, ** p<0.01, *** p<0.001.

FIG. 5. Reprogramming of patient fibroblasts to hiPSCs. FIG. 5A. Experimental schematic for generation of hiPSCs using doxycycline-inducible lentiviral reprogramming vectors. A constitutive CAGGs-rtTA lentivirus drives doxycycline-inducible expression of OCT4, SOX2, KLF4, cMYC, LIN28 and GFP. FIG. 5B, top panel. hiPSCs express NANOG and TRA-1-60. 400×, scale bar 80 μm. FIG. 5B, bottom panel. hiPSCs co-express the transcription factors SOX2 and OCT4. 400×, scale bar 80 μm. FIG. 5C. Representative teratoma assay for pluripotency. Teratomas containing all three germ layers were generated from every hiPSC-line utilized. 200×, scale bar 80 μm. FIG. 5D. Karyotyping of hiPSCs from SCZD and control patients revealed that all patients had normal karyotypes except for patient 2, who had an inversion of chromosome 1 between 1p13.3 and 1q13 that was also present in the HF. FIG. 5E. qPCR analysis of endogenous and lentiviral (LV) pluripotency gene expression in every control and SCZD HF, hiPSC and hiPSC NPC line was performed. Transcripts specific to lentiviral OCT4, SOX2, KLF4 and cMYC were not detected in hiPSC or NPC cell lines.

FIG. 6. Patient-specific hiPSCs, NPCs and neurons. FIG. 6A. Family pedigrees of patients. FIG. 6B. FACS analysis shows ˜80% of hiPSC NPC lines differentiate to MIL tubulin+ cells. Error bars are SE. FIG. 6C. Brightfield images of hiPSC neural differentiation. 100×, scale bar 100 μm. FIG. 6D, top panel. hiPSCs express NANOG and TRA-1-60. DAPI. 100×, scale bar 100 μm. FIG. 6D, middle panel. hiPSC neural progenitor cells (NPCs) express NESTIN and SOX2. 600×, scale bar 100 μm. FIG. 6D, bottom panel. hiPSC neurons express βIII-tubulin and the dendritic marker MAP2AB. 200×, scale bar 100 μm.

FIG. 7. Controls validating observations of decreased neuronal connectivity in SCZD hiPSC neurons. FIG. 7A. Schematic of rabies trans-neuronal tracing. Feature number legend: 301=hiPSC neurons cannot be transduced by ENVA serotyped rabies virus; 302=primary transduction with LV-SYNP-HTG causes expression of TVA receptor; 303=rabies-EnvAΔG-RFP transduces only the cells expressing LV-SYNP-HTG; 304=rabies ENVAΔG-RFP expression in LV-SYNP-HTG labeled hiPSC neuron; 305=monosynaptic transmission of rabies-ENVAΔG-RFP in retrograde direction only; 306=trans-neuronal labeling is measured as the ration of red:green hiPSC neurons. FIG. 7B. Representative images of control and SCZD hiPSC neurons cotransduced with LV-SYNP-HTG and Rabies-ENVAΔG-RFP, 10 days post rabies transduction. All images were captured using identical laser power and gain settings. PHI-tubulin staining of the field is shown below each panel. 400×, scale bar 80 μm. FIG. 7C. Histogram showing relative pixels of control and relative pixels of SCZD hiPSC neurons. hiPSC neurons were transduced with Rabies-ENVAΔG-RFP and either LV-SYNP-HTG or LV-SYNP-HT and assayed either 5, 7 or 10 days post Rabies-ENVAΔG-RFP transduction. Defects in SCZD hiPSC neuronal connectivity are more apparent with time post-rabies transduction, likely reflecting the signal amplification that occurs across the neuronal network when Rabies-ENVAΔG-RFP travels from one SYNP-HTG neuron to a second SYNP-HTG neuron. Error bars are SE. Asterisks used as follows: * p<0.05, *** p<0.001. FIG. 7D. Representative images of control and SCZD hiPSC neurons sequentially transduced with LV-SYNP-HTG and Rabies-ENVAΔG-RFP, or LV-SYNP-HT and Rabies-ENVAΔG-RFP, or Rabies-ENVAΔG-RFP alone. Images taken 10 days post rabies transduction. 400×, scale bar 80 μm. FIG. 7E. Functionally immature one-month-old hiPSC neurons are capable of trans-neuronal tracing. 400×, scale bar 80 μm. FIG. 7F. Representative images demonstrating that trans-neuronal tracing occurs even in the presence of three drugs known to affect synaptic transmission: tetradotoxin, KCl and ryanodine. 400×, scale bar 80 μm.

FIG. 8. Ability of antipsychotic medications to ameliorate decreased neuronal connectivity in SCZD hiPSC neurons. FIG. 8A. Representative images showing improved neuronal connectivity in SCZD three-month-old hiPSC neurons following three-week culture with loxapine. Images taken 10 days post rabies transduction. 200×, scale bar 200 μm. FIG. 8B and FIG. 8C. Histograms showing FACS analysis of control and SCZD three-month-old hiPSC neurons cultured with DMSO, Clozapine, Loxapine, Olanzapine, Risperidone and Thioridazine for the last three weeks of neuronal differentiation and sequentially transduced with LV-SYNP-HTG and Rabies-ENVAΔG-RFP. Only βIII-tubulin-positive events were counted. Error bars are SE. Asterisk used as follows: *** p<0.001.

FIG. 9. Additional controls validating observations of decreased neuronal connectivity in SCZD hiPSC neurons. FIG. 9A and FIG. 9B. Comparison of manual counts (FIG. 9A) of Rabies-ENVAΔG-RFP-labeled and LV-SYNP-HTG-labeled cells and integrated pixel density ratios (FIG. 9B) of Rabies-ENVAΔG-RFP-positive pixels to LV-SYNP-HTG-positive pixels show very similar results between control and SCZD hiPSC neurons. FIG. 9C. Histogram showing relative pixels of averaged control and SCZD hiPSC neurons, when cultured following sequential transduction with LV-SYNP-HTG and Rabies-ENVAΔG-RFP for 10 days. There was no significant difference in the pixel ratio between control and SCZD hiPSC neurons, but there was a significant decrease in the pixel ratios between control and SCZD hiPSC neurons. FIG. 9D. Histogram showing relative pixels of averaged control and SCZD hiPSC neurons, when cultured following sequential transduction with LV-SYNP-HTG and Rabies-ENVAΔG-RFP for 10 days. FIG. 9E. Histogram showing FACS analysis of control and SCZD three-month-old hiPSC neurons cultured on astrocytes and sequentially transduced with LV-TVA-H2BGFP and Rabies-ENVAΔG-RFP. Only βIII-tubulin-positive events were counted. Error bars are SE. Asterisks used as follows: * p<0.05, *** p<0.001.

FIG. 10. Dopaminergic TH-positive SCZD hiPSC neurons. FIG. 10A. Representative images showing TH-positive neurons in three-month-old hiPSC control and SCZD neural populations, costained with βIII-tubulin and DAPI. 200×, scale bar 80 μm. FIG. 10B. Representative images showing single TH-positive neurons in three-month-old hiPSC control and SCZD neural populations, costained with βIII-tubulin. Mature neurons are marked with a LV-SYNP-GFP reporter. 400×, scale bar 80 μm.

FIG. 11. Synaptic protein levels in control and SCZD hiPSC neurons. FIG. 11A. Representative images showing colocalization (indicated by white arrowheads) of VGLUT1-positive and PSD95-positive synaptic densities on neuronal dendrites. 2400×, scale bar 10 μm. FIG. 11B. Representative images showing colocalization (indicated by white arrowheads) of VGAT-positive and GEPH-positive synaptic densities on control and SCZD hiPSC neurons. 2400×, scale bar 10 μm. FIG. 11C. FACS analysis shows ˜30% of hiPSC NPC lines differentiate to GAD65/67+ cells. Error bars are SE. FIG. 11D. Representative images showing colocalization of GAD65/67 and βIII-tubulin in control and SCZD hiPSC neurons. 200×, scale bar 200 μm.

FIG. 12. Decreased neurites and synaptic protein levels in SCZD hiPSC neurons. FIG. 12A. Representative images of rare labeling of individual hiPSC neurons by low titer LV-SYNP-GFP. 800×, scale bar 20 μm. Neurites indicated by white arrows. FIG. 12B. Histogram showing decreased neurites in SCZD hiPSC neurons. FIG. 12C. Histogram showing a trend of decreased PSD95 synaptic density in SCZD hiPSC neurons. FIG. 12D-I. Histograms of synapse protein levels relative to MAP2AB for control and SCZD hiPSC neurons. Synaptic proteins assayed include SYN (FIG. 12D), VGLUT1 (FIG. 12E), GLUR1 (FIG. 12F), PSD95 (FIG. 12G), VGAT (FIG. 12H) and GEPH (FIG. 12I). Error bars are SE. Asterisks used as follows: *** p<0.001.

FIG. 13. Calcium transient analysis shows no difference in basal spontaneous activity between control and SCZD hiPSC neurons. FIG. 13A. Following incubation with the calcium binding dye Fluo-4AM, hiPSC neurons show spontaneous changes in Fluo-4AM fluorescence. Frames of a calcium time-lapse movie of a control hiPSC neuron culture at 0, 15, 30, 60 and 90 seconds. 13 ROIs with fluctuating calcium levels throughout movie are numbered. 100×, scale bar 400 μm. FIG. 13B. Calcium traces (FIG. 13B, left panel), plotting fluorescent intensity versus time, for individual ROIs in the movie shown above. One trace is shown per ROI. Spike events (FIG. 13B, middle panel) are automatically identified throughout 3,000 frames of a 90-second movie. The outline indicates spike events, which are identified based on the amplitude and slope (dF/F) of the calcium trace. Raster plots (FIG. 13B, right panel) of spike events occurring at each ROI over time. FIG. 13C. Histogram showing no difference between the spike amplitude of spontaneous calcium transients of control and SCZD hiPSC neurons. FIG. 13D. Histogram showing no difference between the total numbers of spontaneous calcium transients per total number of ROIs in cultures of control and SCZD hiPSC neurons. FIG. 13E. Representative analysis of synchronized and unsynchronized spontaneous calcium transient activity. Calcium traces (FIG. 13E, left panel), spike events (FIG. 13E, middle panel) and raster plots (FIG. 13E, right panel) of spike events occurring at each ROI over time are shown. FIG. 13F. Histogram showing no change in percentage synchronicity (total synchronized events per total events) between control and SCZD hiPSC neurons. FIG. 13G. Histogram showing no change in maximum percentage synchronicity (maximum number of ROIs involved in a synchronized event per total number of ROIs) between control and SCZD hiPSC neurons. Error bars are SE.

FIG. 14. Microarray gene analysis of control and SCZD hiPSC neurons. FIG. 14A. Heat map showing differential expression of 596 unique genes (271 upregulated and 325 downregulated) showing greater than 1.30-fold expression changes between SCZD and control hiPSC neurons. FIG. 14B. Principle component analysis of gene expression of three independent differentiations of hiPSC neurons from each of four control and four SCZD patients. FIG. 14C. qPCR validation of altered expression of GRIN2A, GRM7, DRD2, PDE4D, and LEF1, as well as response to three weeks of treatment with Loxapine (striped bars) in six-week-old hiPSC neurons. Asterisks used as follows: *** p<0.001.

FIG. 15. Genotyping of patients and gene expression analysis in hiPSC neurons. FIG. 15A. CNV analysis of SCZD patients. No CNVs in genes already implicated in SCZD or BD were identified in families 1 (patient 1) or 2 (patients 2 and 3). Patient 4 and 5 (family 3) showed numerous mutations, including deletion of the first exon of NRG3 isoform 2, deletions of CYP2C19 and GALNT11, and intergenic duplication of GABARB2-GABARA6. FIG. 15B. qPCR analysis for three candidate genes identified by CNV analysis reveals that genotype did not accurately predict gene expression changes in 1-month-old hiPSC neurons. FIG. 15C. CNV data showing the NRG3 deletion in patients 4 and 5 was likely inherited from the unaffected mother. FIG. 15D. qPCR reveals decreased NRG3 and increased NRG1 expression in 1-month-old hiPSC neurons in all patients relative to controls, irrespective of CNV status. Error bars are SE. Asterisks used as follows: * p<0.05, ** p<0.01, *** p<0.001.

FIG. 16. RNA expression analysis of SCZD hiPSC neurons, in untreated and Loxapine-treated conditions. Heat map showing differential expression of 3467 unique genes (1172 upregulated and 2295 downregulated) showing greater than 2.0-fold expression changes between SCZD and control hiPSC neurons.

FIG. 17. RNA expression analysis of SCZD hiPSC neurons, in untreated and Loxapine-treated conditions. FIG. 17A. GO analysis revealed the pathways most significantly affected in SCZDhiPSC neurons following treatment with Loxapine. Specifically, a number of genes implicated in cytoskeleton remodeling and signal transduction were identified. FIG. 17B. Heat maps showing microarray expression profiles of altered expression of a number of cytoskeleton remodeling genes.

FIG. 18. Increased rate of neural migration in SCZD hiPSC NPCs. FIG. 18A. Representative images of NPCs taken during a scratch migration assay. Brightfield and fluorescence images of lentiviral CAG-GFP transfected NPCs were taken every hour for up to 7 days—images shown were taken 0 hours and 100 hours post scratch. FIG. 18B. Histograms showing increasedmigration in SCZD hiPSC NPCs. Top histogram evaluates average speed by dividing the width of the initial scratch by the amount of time required to fill the gap. The bottom histogram calculates maximum speed of NPC migration by determining the rate of change of integrated pixel intensity within the scratch area over each five hour period and reporting the maximum rate. Error bars are SE. Asterisks used as follows: *** p<0.001.

FIG. 19. Altered cellular proliferation or cell cycle dynamics does not explain increased neural migration of SCZD hiPSC NPCs. FIG. 19A. Histogram showing no significant differences between the doubling time of control and SCZD hiPSC NPCs, when calculated by daily cell counts over a 7-day period. FIG. 19B. Histogram showing the cell cycle distribution of control and SCZD hiPSC NPC. There is no significant difference in the percentage of cells in G1, S or G2 between control and SCZD hiPSC NPC. Error bars are SD (FIG. 19A) and SE (FIG. 19B).

FIG. 20. Decreased WNT activity in SCZD hiPSC NPCs. Histogram showing decreased WNT reporter (TOPFLASH) activity relative to total protein content in SCZD hiPSC NPCs. Error bars are SE. Asterisks used as follows: ** p<0.01

DETAILED DESCRIPTION OF THE INVENTION I. Definitions

The following definitions are provided to facilitate understanding of certain terms used frequently herein and are not meant to limit the scope of the present disclosure.

The term “gene” means the segment of DNA involved in producing a protein; it includes regions preceding and following the coding region (leader and trailer) as well as intervening sequences (introns) between individual coding segments (exons). The leader, the trailer as well as the introns include regulatory elements that are necessary during the transcription and the translation of a gene. Further, a “protein gene product” is a protein expressed from a particular gene.

The word “protein” denotes an amino acid polymer or a set of two or more interacting or bound amino acid polymers.

The word “expression” or “expressed” as used herein in reference to a gene means the transcriptional and/or translational product of that gene. The level of expression of a DNA molecule in a cell may be determined on the basis of either the amount of corresponding mRNA that is present within the cell or the amount of protein encoded by that DNA produced by the cell (Sambrook et al., 1989 Molecular Cloning: A Laboratory Manual, 18.1-18.88). Expression of a transfected gene can occur transiently or stably in a cell. During “transient expression” the transfected gene is not transferred to the daughter cell during cell division. Since its expression is restricted to the transfected cell, expression of the gene is lost over time. In contrast, stable expression of a transfected gene can occur when the gene is co-transfected with another gene that confers a selection advantage to the transfected cell. Such a selection advantage may be a resistance towards a certain toxin that is presented to the cell. Expression of a transfected gene can further be accomplished by transposon-mediated insertion into to the host genome. During transposon-mediated insertion the gene is positioned between two transposon linker sequences that allow insertion into the host genome as well as subsequent excision.

The term “transfection” or “transfecting” is defined as a process of introducing nucleic acid molecules into a cell. The introduction may be accomplished by non-viral or viral-based methods. The nucleic acid molecules may be gene sequences encoding complete proteins or functional portions thereof. Non-viral methods of transfection include any appropriate transfection method that does not use viral DNA or viral particles as a delivery system to introduce the nucleic acid molecule into the cell. Exemplary non-viral transfection methods include calcium phosphate transfection, liposomal transfection, nucleofection, sonoporation, transfection through heat shock, magnetifection and electroporation. In some embodiments, the nucleic acid molecules are introduced into a cell using electroporation following standard procedures well known in the art. For viral-based methods of transfection any useful viral vector may be used in the methods described herein. Examples for viral vectors include, but are not limited to retroviral, adenoviral, lentiviral and adeno-associated viral vectors. In some embodiments, the nucleic acid molecules are introduced into a cell using a retroviral vector following standard procedures well known in the art.

A “cell culture” is a population of cells residing outside of an organism. These cells are optionally primary cells isolated from a cell bank, animal, or blood bank, or secondary cells that are derived from one of these sources and have been immortalized for long-lived in vitro cultures.

A “somatic cell” is a cell forming the body of an organism. Somatic cells include cells making up organs, skin, blood, bones and connective tissue in an organism, but not germline cells.

A “stem cell” is a cell characterized by the ability of self-renewal through mitotic cell division and the potential to differentiate into a tissue or an organ. Among mammalian stem cells, embryonic and somatic stem cells can be distinguished. Embryonic stem cells reside in the blastocyst and give rise to embryonic tissues, whereas somatic stem cells reside in adult tissues for the purpose of tissue regeneration and repair.

The term “pluripotent” or “pluripotency” refers to cells with the ability to give rise to progeny that can undergo differentiation, under appropriate conditions, into cell types that collectively exhibit characteristics associated with cell lineages from the three germ layers (endoderm, mesoderm, and ectoderm). Pluripotent stem cells can contribute to tissues of a prenatal, postnatal or adult organism. A standard art-accepted test, such as the ability to form a teratoma in 8-12 week old SCID mice, can be used to establish the pluripotency of a cell population. However, identification of various pluripotent stem cell characteristics can also be used to identify pluripotent cells.

“Pluripotent stem cell characteristics” refer to characteristics of a cell that distinguish pluripotent stem cells from other cells. Expression or non-expression of certain combinations of molecular markers are examples of characteristics of pluripotent stem cells. More specifically, human pluripotent stem cells may express at least some, and optionally all, of the markers from the following non-limiting list: SSEA-3, SSEA-4, TRA-1-60, TRA-1-81, TRA-2-49/6E, ALP, Sox2, E-cadherin, UTF-1, Oct4, Lin28, Rex1, and Nanog. Cell morphologies associated with pluripotent stem cells are also pluripotent stem cell characteristics.

An “induced pluripotent stem cell” refers to a pluripotent stem cell artificially (e.g. non-naturally, in a laboratory setting) derived from a non-pluripotent cell. A “non-pluripotent cell” can be a cell of lesser potency to self-renew and differentiate than a pluripotent stem cell. Cells of lesser potency can be, but are not limited to adult stem cells, tissue specific progenitor cells, primary or secondary cells. An adult stem cell is an undifferentiated cell found throughout the body after embryonic development. Adult stem cells multiply by cell division to replenish dying cells and regenerate damaged tissue. Adult stem cells have the ability to divide and create another like cell and also divide and create a more differentiated cell. Even though adult stem cells are associated with the expression of pluripotency markers such as Rex1, Nanog, Oct4 or Sox2, they do not have the ability of pluripotent stem cells to differentiate into the cell types of all three germ layers. Adult stem cells have a limited potency to self renew and generate progeny of distinct cell types. Without limitation, an adult stem cell can be a hematopoietic stem cell, a cord blood stem cell, a mesenchymal stem cell, an epithelial stem cell, a skin stem cell or a neural stem cell. A tissue specific progenitor refers to a cell devoid of self-renewal potential that is committed to differentiate into a specific organ or tissue. A primary cell includes any cell of an adult or fetal organism apart from egg cells, sperm cells and stem cells. Examples of useful primary cells include, but are not limited to, skin cells, bone cells, blood cells, cells of internal organs and cells of connective tissue. A secondary cell is derived from a primary cell and has been immortalized for long-lived in vitro cell culture.

The term “reprogramming” refers to the process of dedifferentiating a non-pluripotent cell (e.g., an origin cell) into a cell exhibiting pluripotent stem cell characteristics (e.g., a human induced pluripotent stem cell).

Where appropriate the expanding transfected derived stem cell may be subjected to a process of selection. A process of selection may include a selection marker introduced into a an induced pluripotent stem cell upon transfection. A selection marker may be a gene encoding for a polypeptide with enzymatic activity. The enzymatic activity includes, but is not limited to, the activity of an acetyltransferase and a phosphotransferase. In some embodiments, the enzymatic activity of the selection marker is the activity of a phosphotransferase. The enzymatic activity of a selection marker may confer to a transfected induced pluripotent stem cell the ability to expand in the presence of a toxin. Such a toxin typically inhibits cell expansion and/or causes cell death. Examples of such toxins include, but are not limited to, hygromycin, neomycin, puromycin and gentamycin. In some embodiments, the toxin is hygromycin. Through the enzymatic activity of a selection maker a toxin may be converted to a non-toxin, which no longer inhibits expansion and causes cell death of a transfected induced pluripotent stem cell. Upon exposure to a toxin a cell lacking a selection marker may be eliminated and thereby precluded from expansion.

Identification of the induced pluripotent stem cell may include, but is not limited to the evaluation of the afore mentioned pluripotent stem cell characteristics. Such pluripotent stem cell characteristics include without further limitation, the expression or non-expression of certain combinations of molecular markers. Further, cell morphologies associated with pluripotent stem cells are also pluripotent stem cell characteristics.

The term “hiPSC-derived neural cell” refers to a neural progenitor cell (NPC) or a mature neuron that has been derived (e.g., differentiated) from a hiPSC cell in vitro. The hiPSCs can be differentiated by any appropriate method known in the art (e.g., Marchetto, M. C. et al., Cell Stem Cell, 3, 649-657 (2008); Yeo, G. W. et al., PLoS Comput Biol, 3, 1951-1967 (2007)).

A neural progenitor is a cell that has a tendency to differentiate into a neural cell and does not have the pluripotent potential of a stem cell. A neural progenitor is a cell that is committed to the neural lineage and is characterized by expressing one or more marker genes that are specific for the neural lineage. Examples of neural lineage marker genes are N-CAM, the intermediate-filament protein nestin, SOX2, vimentin, A2B5, and the transcription factor PAX-6 for early stage neural markers (i.e. neural progenitors); NF-M, MAP-2AB, synaptosin, glutamic acid decarboxylase, βIII-tubulin and tyrosine hydroxylase for later stage neural markers (i.e. differentiated neural cells). Neural differentiation may be performed in the absence or presence of co-cultured astrocytes.

The term “schizophrenia marker function” means any appropriate genetic or physiological (phenotypic) criteria that is more prevalent and/or pronounced in cells obtained or derived from a schizophrenic subject than in cells obtained or derived from a subject without schizophrenia.

For specific proteins described herein (e.g., Sox2, KLF4, cMYC), the named protein includes any of the protein's naturally occurring forms, or variants that maintain the protein transcription factor activity (e.g., within at least 50%, 80%, 90%, 95%, 96%, 97%, 98%, 99% or 100% activity compared to the native protein). In some embodiments, variants have at least 90%, 95%, 96%, 97%, 98%, 99% or 100% amino acid sequence identity across the whole sequence or a portion of the sequence (e.g. a 50, 100, 150 or 200 continuous amino acid portion) compared to a naturally occurring form. In other embodiments, the protein is the protein as identified by its NCBI sequence reference. In other embodiments, the protein is the protein as identified by its NCBI sequence reference or functional fragment thereof.

As used herein, the terms “prevent” and “treat” are not intended to be absolute terms. Treatment can refer to any delay in onset or prevention, e.g., reduction in the frequency or severity of symptoms, amelioration of symptoms, improvement in patient comfort, reduction in skin inflammation, and the like. The effect of treatment can be compared to an individual or pool of individuals not receiving a given treatment, or to the same patient before, or after cessation of, treatment.

“Treating” or “treatment” as used herein (and as well-understood in the art) also broadly includes any approach for obtaining beneficial or desired results in a subject's condition, including clinical results. Beneficial or desired clinical results can include, but are not limited to, alleviation or amelioration of one or more symptoms or conditions, diminishment of the extent of a disease, stabilizing (i.e., not worsening) the state of disease, prevention of a disease's transmission or spread, delay or slowing of disease progression, amelioration or palliation of the disease state, diminishment of the reoccurrence of disease, and remission, whether partial or total and whether detectable or undetectable. In other words, “treatment” as used herein includes any cure, amelioration, or prevention of a disease. Treatment may prevent the disease from occurring; inhibit the disease's spread; relieve the disease's symptoms, fully or partially remove the disease's underlying cause, shorten a disease's duration, or do a combination of these things.

The “subject” as used herein is a subject in need of treatment for schizophrenia. The subject is preferably a mammal and is most preferably a human, but also may include laboratory, pet, domestic, or livestock animals.

The term “disease” refers to any deviation from the normal health of a mammal and includes a state when disease symptoms are present, as well as conditions in which a deviation (e.g., infection, gene mutation, genetic defect, etc.) has occurred, but symptoms are not yet manifested. According to the present invention, the methods disclosed herein are suitable for use in a patient that is a member of the Vertebrate class, Mammalia, including, without limitation, primates, livestock and domestic pets (e.g., a companion animal). Typically, a patient will be a human patient.

As used herein, “administering” means any appropriate method of providing a treatment to a patient such as oral (“po”) administration, administration as a suppository, topical contact, intravenous (“iv”), intraperitoneal (“ip”), intramuscular (“im”), intralesional, intranasal or subcutaneous (“sc”) administration, or the implantation of a slow-release device e.g., a mini-osmotic pump or erodible implant, to a subject. Administration is by any appropriate route including parenteral and transmucosal (e.g., oral, nasal, vaginal, rectal, or transdermal). Parenteral administration includes, e.g., intravenous, intramuscular, intra-arteriole, intradermal, subcutaneous, intraperitoneal, intraventricular, and intracranial. Other modes of delivery include, but are not limited to, the use of liposomal formulations, intravenous infusion, transdermal patches, etc.

The terms “systemic administration” and “systemically administered” refer to a method of administering a compound or composition to a mammal so that the compound or composition is delivered to sites in the body, including the targeted site of pharmaceutical action, via the circulatory system. Systemic administration includes, but is not limited to, oral, intranasal, rectal and parenteral (i.e., other than through the alimentary tract, such as intramuscular, intravenous, intra-arterial, transdermal and subcutaneous) administration.

As used herein, “increase,” or “increasing” in reference to a treated cell means an increase in a measured parameter (e.g., activity, expression, signal transduction, neuron degeneration) in a treated cell (tissue or subject) in comparison to an untreated cell (tissue or subject). A comparison can also be made of the same cell or tissue or subject between before and after treatment. The increase is sufficient to be detectable. In some embodiments, the increase in the treated cell is at least about 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 1-fold, 2-fold, 3-fold, 4-fold or more in comparison to an untreated cell.

As used herein, “inhibit,” “prevent”, “reduce,” “inhibiting,” “preventing” or “reducing” in reference to a treated cell are used interchangeably herein. These terms refer to the decrease in a measured parameter (e.g., activity, expression, signal transduction, neuron degeneration) in a treated cell (tissue or subject) in comparison to an untreated cell (tissue or subject). A comparison can also be made of the same cell or tissue or subject between before and after treatment. The decrease is sufficient to be detectable. In some embodiments, the decrease in the treated cell is at least about 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, or completely inhibited in comparison to an untreated cell. In some embodiments the measured parameter is undetectable (i.e., completely inhibited) in the treated cell in comparison to the untreated cell.

The term “in vivo” refers to an event that takes place in a subject's body.

The term “in vitro” refers to an event that takes places outside of a subject's body. For example, an in vitro assay encompasses any assay run outside of a subject assay. In vitro assays encompass cell-based assays in which cells alive or dead are employed. In vitro assays also encompass a cell-free assay in which no intact cells are employed.

The terms “effective amount,” “therapeutically effective amount” or “pharmaceutically effective amount” as used herein refers to that amount of the therapeutic agent sufficient to ameliorate one or more aspects of the disorder (e.g., schizophrenia). The result can be reduction and/or alleviation of the signs, symptoms, or causes of a disease, or any other desired alteration of a biological system. For example, an “effective amount” for therapeutic uses is the amount of a composition required to provide a clinically significant decrease in schizophrenia. For example, for the given aspect (e.g., length of incidence), a therapeutically effective amount will show an increase or decrease of at least 5%, 10%, 15%, 20%, 25%, 40%, 50%, 60%, 75%, 80%, 90%, or at least 100%. Therapeutic efficacy can also be expressed as “-fold” increase or decrease. For example, a therapeutically effective amount can have at least a 1.2-fold, 1.5-fold, 2-fold, 5-fold, or more effect over a control. An appropriate “effective” amount in any individual case may be determined using techniques, such as a dose escalation study.

The term “schizophrenic” refers to a subject that has been clinically diagnosed with schizophrenia, displays one or more schizophrenia symptoms or has a family history of schizophrenia. A subject having a family history of schizophrenia is also referred to herein as a “pre-symptomatic” subject or “pre-symptomatic schizophrenic.” A pre-symptomatic subject is a subject that has not developed schizophrenia symptoms yet. A pre-symptomatic subject may be a subject having a family history of schizophrenia (i.e. a genetic schizophrenic). Non-limiting examples of schizophrenia symptoms include physiologic symptoms (e.g., auditory hallucinations, paranoia, delusions, disorganized speech and thinking, psychomotor agitation, depression; see also Diagnostic and Statistical Manual of Mental Disorders, Fourth Edition, 2000, American Psychiatric Association, Washington, D.C. (“DSM-IV”) and genetic symptoms (e.g., aberrant gene expression of one or more genes associated with schizophrenia. Non-limiting examples of genes associated with schizophrenia are listed in Table 5 (e.g., AQP4, HEY2, GRIK1, GFAP, SPP1, SPARCL1). In some embodiments, a schizophrenic subject is a subject not clinically diagnosed with schizophrenia. In other embodiments, a schizophrenic subject is a subject displaying one or more schizophrenia symptoms. In other embodiments, a schizophrenic subject is a subject having a family history of schizophrenia. In other embodiments, a schizophrenic subject is a pre-symptomatic subject (i.e. a pre-symptomatic schizophrenic).

II. Methods

The methods according to the embodiments provided herein inter alia, are useful in the area of schizophrenia drug development, diagnosis and personalized medicine.

A. Methods of Screening for Schizophrenia Compounds

In one aspect, a method of determining whether a test compound is capable of improving a schizophrenia marker function in a hiPSC-derived neural cell is provided. The method includes contacting a test compound with a hiPSC-derived neural cell derived from a schizophrenic subject. The hiPSC-derived neural cell exhibits a schizophrenia marker function at a first level in the absence of the test compound. Then, a second level of the schizophrenia marker function is determined in the presence of the test compound. The second level is compared to a control level. A smaller difference between the second level and the control level than between the first level and the control level indicates that the test compound is capable of improving the schizophrenia marker function. A control level of a schizophrenia marker function as provided herein refers to a level of the schizophrenia marker function in a control cell. A control cell is a cell that is derived from a non-schizophrenic (e.g., healthy) subject or a pre-symptomatic subject. In some embodiments, the control level is a level lower than the first level. In other embodiments, the control level is a level higher than the first level. In some embodiments, the control level of a schizophrenia marker function is a level of the schizophrenia marker function in a healthy subject. In other embodiments, the control level of a schizophrenia marker function is a level of the schizophrenia marker function in a pre-symptomatic subject. In some embodiments, the smaller difference indicates that the schizophrenic subject is responsive to the test compound. Thus, where the subject is not responsive to the test compound the difference between the second level of a schizophrenia marker function and the control level is bigger than the difference between the first level and the control level.

In one embodiment, a smaller difference indicates that the schizophrenic subject is responsive to the test compound. A subject is “responsive” when the subject experiences a reduction in one or more schizophrenic symptoms. In this way, the screening methods can be used to assess the efficacy of various test compounds on neural cells modeled from the subject's own cells in vitro, thereby identifying treatment regimens that may be most effective to the particular subject to be treated without subjecting the subject to multiple experimental treatment regimens, the side effects accompanying any particular treatment regimen, as well as side effects associated with beginning a new treatment regimen and changing treatment regimens.

Accordingly, in one embodiment, where the test compound is found to be capable of improving a schizophrenia marker function in a hiPSC-derived neural cell, the method further comprises administering an effective amount of the test compound (e.g., a test compound identified as described above) to the schizophrenic subject in need of treatment for schizophrenia (e.g., the subject from whom the hiPSCs were derived for the screening method).

In the methods provided herein, a test compound may be contacted with a hiPSC-derived neural cell and/or administered to a subject in need of treatment for schizophrenia. In some embodiments, the compound may be a known compound such as typical antipsychotics, atypical antipsychotics, or combinations thereof. In other embodiments, the test compound is clozapine, loxapine, olanzapine, risperidone, thioridazine, perphenazine, aripiprazole, iloperidone, ziprasidone, paliperidone, lurasidone, molindone, asenapine, mesoridazine, quetiapine, or trifluoperazine. In other embodiments, the compound is clozapine, loxapine, olanzapine, risperidone, and thioridazine. In some embodiments, the compound is loxapine. In another embodiment, the compound is not currently approved for the indication of schizophrenia.

The methods provided herein may be used for identifying test compounds that may be useful for treating schizophrenia, for identifying test compounds that are currently marketed for other psychotic or non-psychotic indications but may also be useful for treating schizophrenia, and/or for identifying compounds that are currently marketed for schizophrenia that may be useful for treating schizophrenia in a particular subject (e.g., personalized medicine applications).

Generation of Human Induced Pluripotent Stem Cell-Derived Neural Cells

The methods described herein employ a hiPSC-derived neural cell. In any of the methods, the hiPSC-derived neural cell can be produced by: a) obtaining a primary cell from a control subject (i.e., non-schizophrenic) and/or a schizophrenic subject, b) reprogramming the primary cell to form a hiPSC (e.g., through viral transfection), and c) allowing the hiPSC to differentiate and/or promoting differentiation of the hiPSC in vitro to form a hiPSC-derived neural cell. The primary cell can be any somatic cell. In some embodiments, the primary cell is a fibroblast cell. In some embodiments, the primary cell is obtained from a schizophrenic subject. In some embodiments, the method includes (i) reprogramming a fibroblast cell thereby forming a fibroblast-derived hiPSC; and (ii) differentiating the fibroblast-derived hiPSC thereby forming the hiPSC-derived neural cell. Differentiating the fibroblast-derived hiPSC may include expansion of fibroblast cell after transfection, optional selection of transfected cells and identification of resulting pluripotent stem cells. Expansion as used herein includes the production of progeny cells by a transfected fibroblast cell under conditions well know in the art (Soldner, F. et al. Cell 136:964-977 (2009); Yamanaka, S. Cell 137:13-17 (2009)). Expansion may occur in the presence of suitable media and cellular growth factors. Cellular growth factors are agents which cause cells to migrate, differentiate, transform or mature and divide. Cellular growth factors are polypeptides which can usually be isolated from various normal and malignant mammalian cell types. Some growth factors can also be produced by genetically engineered microorganisms, such as bacteria (E. coli) and yeasts. Cellular growth factors may be supplemented to the media and/or may be provided through co-culture with irradiated embryonic fibroblast that secrete such cellular growth factors. Examples of cellular growth factors include, but are not limited to, FGF, bFGF2, and EGF.

Where appropriate the expanding fibroblast cell may be subjected to a process of selection. A process of selection may include a selection marker introduced into a fibroblast cell upon transfection. A selection marker may be a gene encoding for a polypeptide with enzymatic activity. The enzymatic activity includes, but is not limited to, the activity of an acetyltransferase and a phosphotransferase. In some embodiments, the enzymatic activity of the selection marker is the activity of a phosphotransferase. The enzymatic activity of a selection marker may confer to a transfected neural stem cell the ability to expand in the presence of a toxin. Such a toxin typically inhibits cell expansion and/or causes cell death. Examples of such toxins include, but are not limited to, hygromycin, neomycin, puromycin and gentamycin. In some embodiments, the toxin is hygromycin. Through the enzymatic activity of a selection maker a toxin may be converted to a non-toxin which no longer inhibits expansion and causes cell death of a transfected neural stem cell. Upon exposure to a toxin a cell lacking a selection marker may be eliminated and thereby precluded from expansion.

Identification of the hiPSC may include, but is not limited to the evaluation of the afore mentioned pluripotent stem cell characteristics. Such pluripotent stem cell characteristics include without further limitation, the expression or non-expression of certain combinations of molecular markers. Further, cell morphologies associated with pluripotent stem cells are also pluripotent stem cell characteristics.

In some embodiments, the hiPSC exhibits normal expression of endogenous pluripotency genes. In another embodiment, the hiPSC represses viral genes. In another embodiment, the hiPSC both exhibits normal expression of endogenous pluripotency genes and repression of viral genes.

Schizophrenia Marker Functions

The hiPSC-derived neural cells as described above may be used in any of the methods disclosed herein as appropriate. The methods described herein may also include assessing or measuring one or more schizophrenia marker functions. In one embodiment, the schizophrenia marker function is a level of gene expression. As provided herein, any appropriate genetic or physiological (e.g., phenotypic) criteria that is more prevalent and/or pronounced in cells obtained or derived from a schizophrenic subject than in cells obtained or derived from a non-schizophrenic subject is a schizophrenia marker function. In one embodiment, the schizophrenia marker function is a level of protein production. In another embodiment, the schizophrenia marker function is a structural characteristic of a neural cell. In another embodiment, the schizophrenia marker function is a characteristic of intracellular relation/communication. In some embodiments, the schizophrenia marker function is a number of neurites extending from the hiPSC-derived neural cell, a level of synaptic proteins expressed by the hiPSC-derived neural cell, a level of PSD95 expressed by the hiPSC-derived neural cell, a level of synaptic density of the hiPSC-derived neural cell, a level of neural connectivity of the hiPSC-derived neural cell, a level of synaptic plasticity of the hiPSC-derived neural cell, a level of NRG1 expressed by the hiPSC-derived neural cell, a level of a glutamate receptor expressed by the hiPSC-derived neural cell, a level of a neuregulin pathway component expressed by the hiPSC-derived neural cell, a level of a synaptic protein expressed by the hiPSC-derived neural cell, a level of a cAMP component expressed by the hiPSC-derived neural cell, a level of a calcium signaling pathway component expressed by the hiPSC-derived neural cell, a level of a Wnt signaling pathway component expressed by the hiPSC-derived neural cell, a level of a Notch growth factor expressed by the hiPSC-derived neural cell, a level of neural migration by the hiPSC-derived neural cell or a level of a cell adhesion component by the hiPSC-derived neural cell. In other embodiments, the schizophrenia marker function is a number of neurites extending from the hiPSC-derived neural cell, a level of synaptic proteins expressed by the hiPSC-derived neural cell, a level of PSD95 expressed by the hiPSC-derived neural cell, a level of synaptic density of the hiPSC-derived neural cell, a level of neural connectivity of the hiPSC-derived neural cell, a level of synaptic plasticity of the hiPSC-derived neural cell, a level of NRG1 expressed by the hiPSC-derived neural cell, a level of a glutamate receptor expressed by the hiPSC-derived neural cell, a level of a neuregulin pathway component expressed by the hiPSC-derived neural cell, a level of a synaptic protein expressed by the hiPSC-derived neural cell, a level of a cAMP component expressed by the hiPSC-derived neural cell, a level of a calcium signaling pathway component expressed by the hiPSC-derived neural cell, a level of a Wnt signaling pathway component expressed by the hiPSC-derived neural cell, a level of a Notch growth factor expressed by the hiPSC-derived neural cell, a level of neural migration by the hiPSC-derived neural cell and a level of a cell adhesion component by the hiPSC-derived neural cell.

When the schizophrenia marker function is the number of neurites extending from the hiPSC-derived neural cell, a decrease in the number of neurites is indicative of an increased likelihood and/or severity of schizophrenia.

Synaptic density can be measured, for example, by identifying colocalized synaptic puncta of VGLUT1 and PSD95, thresholding on size and then manually counting large colocalized puncta along a given length of neurite. Decreased synaptic density is indicative of an increased likelihood and/or severity of schizophrenia.

Neural connectivity can be measured by, for example, using trans-synaptic labeling using tracers (e.g., rabies viral trans-synaptic labeling). Decreased trans-synaptic labeling is indicative of an increased likelihood and/or severity of schizophrenia.

Synaptic plasticity can be measured by, for example, measuring variations in intracellular calcium levels.

For gene expression levels (e.g., NRG3, NRG2, NRG1, PSD95, and PSD93), a decrease in expression is indicative of an increased likelihood and/or severity of schizophrenia.

Glutamate receptors are synaptic receptors located primarily on the membranes of neural cells. They include ionotropic (e.g., AMPA, Kainate, and NMDA families) and metabotropic (e.g., groups 1, 2, and 3) receptors.

The neuregulins are a family of structurally-related proteins that are part of the EGF family of proteins. Neuregulin pathway components include the neuregulins themselves (e.g., NRG1 and any of its isoforms, NRG2, NRG3, or NRG4) as well as proteins that interact with the neuregulins and nucleic acids that encode either the neuregulins or their associated proteins. Exemplary neuregulin pathway components include, but are not limited to ERBB2, ERBB3, ERBB4, and LIMK1.

A synaptic protein is any appropriate protein that affects synaptic transmission. In particular, synaptic proteins include regulators of synaptic transmission are palmitoylated proteins that are concentrated at pre- or postsynaptic sites. On the presynaptic side, palmitoylated proteins regulate synaptic vesicle fusion and neurotransmitter synthesis and release. These include several members of the synaptotagmin family, synaptobrevin 2 and SNAP25 (synaptosomal-associated protein, 25 kDa), and GAD65 (glutamic acid decarboxylase, 65 kDa), which synthesizes the inhibitory neurotransmitter GABA (-aminobutyric acid). Palmitoylated presynaptic proteins also include the 2A-subunit of the voltage-dependent calcium channel, and the -subunit of sodium channels. GAP43 (growth-associated protein 43), paralemmin and NCAM140 (neural cell-adhesion molecule) are palmitoylated proteins that are associated with axonal growth cones. RhoB (Ras homologue B) and Tc10 are small GTPases that regulate cytoskeletal dynamics. On the postsynaptic side, many receptors are palmitoylated, including G-protein-coupled receptors (GPCRs), the METABOTROPIC glutamate receptor subunit mGluR4 and the kainate receptor subunit GluR6. Numerous downstream signaling enzymes are also palmitoylated, including the G-protein-subunit, Fyn (a member of the Src family of non-receptor tyrosine kinases) and a Ras small GTPase. By scaffolding receptors and enzymes, palmitoylated PDZ proteins have an important role in the assembly of postsynaptic signaling pathways. Palmitoylated PDZ proteins at the synapse include the postsynaptic density proteins PSD95 and PSD93, which bind the tails of NMDA (N-methyl-d-asparate) receptors and the AMPA (-amino-3-hydroxy-5-methyl-4-isoxazole propionic acid)-receptor-associated protein stargazin, and GRIP1b (glutamate-receptor-interacting protein 1b) and ABP-L (AMPA-receptor-binding protein-L), which bind the tail of the AMPA receptor subunit GluR2. Alaa El-Din El-Husseini & David S. Bredt. “Protein palmitoylation: a regulator of neural development and function” Nature Reviews Neuroscience 3, 791-802 (2002).

cAMP is derived from adenosine triphosphate (ATP) and used for intracellular signal transduction in many different organisms, conveying the cAMP-dependent pathway. Exemplary cAMP components include, but are not limited to, protein kinase A (PKA), exchange proteins (e.g., Epac1, Epac2), Rap1, epinephrine (adrenaline), G protein, adenylyl cyclase, cAMP receptor protein (CRP, CAP), as well as the lac operon.

Calcium signaling pathway components affect the influx of calcium resulting from activation of ion channels or by indirect signal transduction pathways. Exemplary calcium signaling pathway components include, but are not limited to, phospholipase C (PLC), G-protein couple receptors, PIP2, IP3, IP3 receptor, diacylglycerol (DAG), protein kinase C, “Store Operated Channels” (SOCs), Orai1, STIM1 phospholipase A2 beta, nicotinic acid adenine dinucleotide phosphate (NAADP), STIM 1, calmodulin, and calcium-calmodulin dependent protein kinases.

Exemplary Wnt signaling pathway components include, but are not limited to, WNT1, WNT2, WNT2B, WNT3, WNT3A, WNT4, WNT5A, WNT5B, WNT6, WNT7A, WNT7B, WNT8A, WNT8B, WNT9A, WNT9B, WNT10A, WNT10B, WNT11, and WNT16, as well as cell-surface receptors of the Frizzled family, Dishevelled family proteins, β-catenin, axin, GSK-3, protein APC, as well as TCF/LEF family transcription factors.

Members of the notch signaling pathway include, but are not limited to, NOTCH1, NOTCH2, NOTCH3, and NOTCH4 as well as notch ligands.

Neural cells reside in different areas of the brain during their development. For instance, neural progenitors reside in the developing neocortex and upon development migrate to different areas of the cortex depending on their function. Surprisingly, Applicants have found that schizophrenic neural precursors exhibit an impaired neural migration. The level of neural migration of hiPSC-derived neural cells obtained or derived from a schizophrenic subject (i.e. schizophrenic neural migration) may be higher than the level of neural migration of hiPSC-derived neural cells derived or obtained from a non-schizophrenic subject (i.e. non-schizophrenic neural migration). In some embodiments, the level of schizophrenic neural migration is higher than the level of non-schizophrenic neural migration. When the schizophrenia marker function is a level of neural migration by the hiPSC-derived neural cell, an increase in the level of neural migration is indicative of an increased likelihood and/or severity of schizophrenia.

In some embodiments, the level of a cell adhesion component expressed by the hiPSC-derived neural cell is decreased. When the schizophrenia marker function is a level of a cell adhesion component expressed by the hiPSC-derived neural cell, a decrease in the level of a cell adhesion component expressed by the hiPSC-derived neural cell is indicative of an increased likelihood and/or severity of schizophrenia.

Any one or more of these schizophrenia marker functions can be used in any of the following methods. In another embodiment, a schizophrenia marker function can first be identified by the method of identifying a schizophrenia marker function, described in detail below, and then employed in the methods of screening test compounds and/or methods of diagnosing schizophrenia.

B. Methods of Determining Whether a Subject is Schizophrenic

In one aspect, a method of determining whether a subject is schizophrenic is provided. The method includes determining a level of a schizophrenia marker function in a hiPSC-derived neural cell derived from a subject (a test subject) and comparing the level to a control level. A difference between the determined level and the control level indicates that the subject is schizophrenic. In some embodiments, the method further includes the steps of quantitating the level of the schizophrenia marker function to determine a test quantity, and comparing the test quantity to a control quantity to determine the severity of the subject's schizophrenia. Quantitating the level of the schizophrenia marker function may include quantification of any of the above described schizophrenia marker functions using methods well known in the art (e.g., quantifying the number of neurites of a hiPSC-derived neural cell, measuring synaptic density by quantifying colocalized synaptic puncta of VGLUT1 and PSD95 along a given length of neurite, measuring neural connectivity using trans-synaptic labeling using tracers (e.g., rabies viral trans-synaptic labeling), measuring gene expression levels (e.g., NRG3, NRG2, NRG1, PSD95, and PSD93)). A control quantity refers to the quantitated level of the schizophrenia marker function in a non-schizophrenic cell (e.g., healthy cell). For example, where the schizophrenia marker function is the level of neural connectivity, trans-synaptic labeling as described in the Example section may be used to measure (i) a test quantity of neural connectivity in hiPSC-derived neural cells from a schizophrenic subject and (ii) compare the test quantity to a control quantity which is a quantity of neural connectivity measured in hiPSC-derived neural cells from a non-schizophrenic subject.

In some embodiments, the method further includes the preliminary steps of creating a hiPSC-derived neural cell. As described above, hiPSC-derived neural cells can be made by obtaining a cell (e.g., a fibroblast cell) from the subject. In some embodiments, the cell is a fibroblast cell. The cell is then reprogrammed to form a hiPSC. Then the hiPSC is allowed to differentiate thereby forming a hiPSC-derived neural cell.

In some embodiments, the method further includes treating the subject in need of treatment for schizophrenia. Treating the subject in need of treatment for schizophrenia includes administering to the subject an effective amount of a compound identified using any of the methods provided herein. The compound may be part of a powder, tablet, capsule, liquid, ointment, cream, gel, hydrogel, aerosol, spray, micelle, liposome or any other pharmaceutically acceptable form. One of ordinary skill in the art would readily appreciate that an appropriate vehicle for use with the compounds identified using the methods provided herein should be one that is well tolerated by a recipient of the composition. The vehicle should also readily enable the delivery of the compounds to appropriate target receptors. For example, one of ordinary skill in the art would know to consult Pharmaceutical Dosage Forms and Drug Delivery Systems, by Ansel, et al., Lippincott Williams & Wilkins Publishers; 7th ed. (1999) or a similar text for guidance regarding such formulations. The composition identified using the methods provided herein may be used in a number of ways. For instance, systemic administration may be required in which case the compounds can be formulated into a composition that can be ingested orally in the form of a tablet, capsule or liquid. Alternatively the composition may be administered by injection into the blood stream. Injections may be intravenous (bolus or infusion) or subcutaneous (bolus or infusion). The disclosed compounds can also be administered centrally by means of intracerebral, intracerebroventricular, or intrathecal delivery.

It will be readily appreciated that the amount of a compound required is determined by biological activity and bioavailability which in turn depends on the mode of administration, the physicochemical properties of the compound employed and whether the compound is being used as a monotherapy or in a combined therapy. For combined therapy the compound may be administered in combination with another pharmacological agent, for example, lithium, valproate, or an antidepressant, for example, fluoxetine. The frequency of administration will also be influenced by the above mentioned factors and particularly the half-life of the compound within the subject being treated. One of ordinary skill in the art would appreciate that specific formulations of compositions and precise therapeutic regimes (such as daily doses of the compounds and the frequency of administration) can be determined using known procedures. Such procedures conventionally employed by the pharmaceutical industry include in vivo experimentation and clinical trials.

The methods provided herein may be useful for diagnostic assessments for both symptomatic and asymptomatic (e.g., pre-symptomatic) subjects. As described above a subject is schizophrenic if the subject displays one or more schizophrenic symptoms. A subject that has not been diagnosed with schizophrenia (e.g., pre-symptomatic) but has a family history of schizophrenia is referred to as a schizophrenic subject. The methods may also be used in the area of personalized medicine. For instance, where a subject is in need of treatment for schizophrenia, the most effective and compliant drug specific for this subject can be determined in vitro using the methods provided herein. Without administering the drug to the subject it can be determined whether a drug is appropriate (i.e. effective, causing least side effects) for treatment of schizophrenia in a particular subject. Rather than administering different drugs to a subject sequentially to identify the most effective drug for that particular subject, the methods provided herein allow for simultaneous testing of a plurality of drugs in vitro. Therefore the subject is not subjected to multiple experimental treatment regimens, the side effects accompanying any particular treatment regimen, as well as side effects associated with beginning a new treatment regimen and changing treatment regimens. Further, the progression of a disease state and/or the efficacy of a treatment regimen can be assessed in a single subject in a recurrent, e.g., periodic, manner.

C. Methods of Identifying a Schizophrenia Marker Function

The methods provided herein, inter alia, are useful for identifying new schizophrenia marker functions. In one aspect, a method of identifying a schizophrenia marker function is provided. The method includes obtaining a cell from a schizophrenic subject and reprogramming the cell thereby forming a hiPSC. The hiPSC is allowed to differentiate thereby forming a hiPSC-derived neural cell derived from the schizophrenic subject. A level of a function of the hiPSC-derived neural cell is determined and the level is compared to a control level. A difference between the level and the control level indicates the function is a schizophrenia marker function. The level of a function of a hiPSC-derived neural cell includes any genetic or physiological criteria that is more prevalent and/or pronounced in a neural cell obtained or derived from a schizophrenic subject than in a neural cell obtained or derived from a non-schizphrenic subject. In some embodiments, the cell is a fibroblast cell. The method may include comparisons between: a) a single schizophrenic subject and a single non-schizophrenic subject, b) an average level exhibited by multiple schizophrenic subjects and an average level exhibited by multiple control subjects, or c) a pre-schizophrenic subject and the same subject after the manifestation of schizophrenic symptoms.

D. Methods of Determining Loxapine Marker Functions

Loxapine is a antipsychotic drug, which is primarily used for the treatment of schizophrenia. Loxapine is a dibenzazepine derivative and refers, in the customary sense, to CAS Registry No. 1977-10-2. The methods provided herein can be used to determine whether a subject is responsive to loxapine and whether loxapine is the most effective drug to treat schizophrenia in a particular subject. A loxapine compound as referred to herein is any compound having the same pharmacological properties as loxapine. Examples of loxapine compounds include pharmaceutically acceptable salts of loxapine or any derivatives of loxapine having the same pharmacological properties as loxapine.

In one aspect, a method of determining whether a schizophrenic subject is responsive to treatment with a loxapine compound is provided. The method includes contacting a loxapine compound with a hiPSC-derived neural cell. The hiPSC-derived neural cell is derived from the schizophrenic subject, and the hiPSC-derived neural cell exhibits a loxapine marker function at a first level in the absence of a loxapine compound. Then a second level of the loxapine marker function is determined and the second level is compared to a control level. A smaller difference between the second level and the control level than between the first level and the control level indicates the schizophrenic subject is responsive to treatment with a loxapine compound. The control level is the level of a loxapine marker function of a control cell. A control cell is a cell that is derived from a non-schizophrenic (e.g., healthy) subject or a pre-symptomatic subject. In some embodiments, the control level is a level lower than the first level. In other embodiments, the control level is a level higher than the first level. In some embodiments, the control level of a loxapine marker function is a level of the loxapine marker function in a healthy subject. In other embodiments, the control level of a loxapine marker function is a level of the loxapine marker function in a pre-symptomatic subject. In some embodiments, the smaller difference indicates that the schizophrenic subject is responsive to the loxapine compound. Thus, where the subject is not responsive to the loxapine compound the difference between the second level of a loxapine marker function and the control level is bigger than the difference between the first level and the control level.

A “loxapine marker function” is a schizophrenia marker function that is modified by treatment with a loxapine compound. In some embodiments, the loxapine marker function is a level of a cytoskeleton remodeling component expressed by the hiPSC-derived neural cell, a level of TGF signaling pathway component expressed by the hiPSC-derived neural cell, a level of NRG1 expressed by the hiPSC-derived neural cell, a level of a glutamate receptor expressed by the hiPSC-derived neural cell, a level of neural connectivity of the hiPSC-derived neural cell, or a level of a cell adhesion component expressed by the hiPSC-derived neural cell. In some embodiments, the loxapine marker function is a level of a cytoskeleton remodeling component expressed by the hiPSC-derived neural cell, a level of TGF signaling pathway component expressed by the hiPSC-derived neural cell, a level of NRG1 expressed by the hiPSC-derived neural cell, a level of a glutamate receptor expressed by the hiPSC-derived neural cell, a level of neural connectivity of the hiPSC-derived neural cell, and a level of a cell adhesion component expressed by the hiPSC-derived neural cell.

In some embodiments, the method further includes administering an effective amount of a loxapine compound to the schizophrenic subject in need of treatment for schizophrenia. In some embodiments, the hiPSC-derived neural cell is made by a method including reprogramming a fibroblast cell thereby forming a fibroblast-derived hiPSC and differentiating the fibroblast-derived hiPSC thereby forming the hiPSC-derived neural cell.

In another aspect, a method of determining whether a test compound is capable of improving a loxapine marker function is provided. The method includes contacting a test compound with a hiPSC-derived neural cell. The hiPSC-derived neural cell is derived from a schizophrenic subject, and the hiPSC-derived neural cell exhibits a loxapine marker function at a first level in the absence of the test compound. Then a second level of the loxapine marker function determined and the second level is compared to a control level. A smaller difference between the second level and the control level than between the first level and the control level indicates the test compound is capable of improving the loxapine marker function. In some embodiments, the smaller difference indicates the schizophrenic subject is responsive to the test compound. In some embodiments, the loxapine marker function is a level of a cytoskeleton remodeling component expressed by the hiPSC-derived neural cell, a level of TGF signaling pathway component expressed by the hiPSC-derived neural cell, a level of NRG1 expressed by the hiPSC-derived neural cell, a level of a glutamate receptor expressed by the hiPSC-derived neural cell, a level of neural connectivity of the hiPSC-derived neural cell, or a level of a cell adhesion component expressed by the hiPSC-derived neural cell. In other embodiments, the loxapine marker function is a level of a cytoskeleton remodeling component expressed by the hiPSC-derived neural cell, a level of TGF signaling pathway component expressed by the hiPSC-derived neural cell, a level of NRG1 expressed by the hiPSC-derived neural cell, a level of a glutamate receptor expressed by the hiPSC-derived neural cell, a level of neural connectivity of the hiPSC-derived neural cell, and a level of a cell adhesion component expressed by the hiPSC-derived neural cell.

In other embodiments, the method further includes administering an effective amount of the test compound to the schizophrenic subject in need of treatment for schizophrenia. Methods of treating schizophrenia applicable to the compounds identified through the methods disclosed herein are described in section C.

In some embodiments, the hiPSC-derived neural cell is made by a method including reprogramming a fibroblast cell thereby forming a fibroblast-derived hiPSC and differentiating the fibroblast-derived hiPSC thereby forming the hiPSC-derived neural cell. In some embodiments, the fibroblast cell is obtained from a schizophrenic subject. In some further embodiments, the schizophrenic subject is a pre-symptomatic subject.

III. Examples A. Methodologies

Reprogramming hiPSCs

Control and SCZD HFs were obtained from cell repositories and were reprogrammed with tetracycline-inducible lentiviruses expressing the transcription factors OCT4, SOX2, KLF4, cMYC and LIN28⁷. Lentiviruses were packaged in 293T HEK cells transfected with Polyethylenimine (PEI) (Polysciences). HFs were transduced and then split onto mouse embryonic fibroblasts (mEFs). Cells were switched to HUES media (KO-DMEM (Invitrogen), 10% KO-Serum Replacement (Invitrogen), 10% Plasminate (Talecris), 1× Glutamax (Invitrogen), 1×NEAA (Invitrogen), 1×2 βmercaptoethanol (Sigma) and 20 ng/ml FGF2 (Invitrogen)) and 1 μg/ml Doxycycline (Sigma) was added to HUES media for the first 21-28 days of reprogramming. hiPSCs were generally grown in HUES media: early passage hiPSCs were split through manual passaging, while at higher passages hiPSCs could be enzymatically passaged with 1 mg/ml Collagenase (Sigma).

hiPSC Differentiation to NPCs and Neurons

Embryoid bodies were generated from hiPSCs and then transferred to nonadherent plates (Corning). Colonies were maintained in suspension in N2 media (DMEM/F12 (Invitrogen), 1×N2 (Invitrogen)) for 7 days and then plated onto polyornithine (PORN)/Laminin-coated plates. Visible rosettes formed within 1 week and were manually dissected and cultured in NPC media (DMEM/F12, 1×N2, 1×B27-RA (Invitrogen), 1 μg/ml Laminin (Invitrogen) and 20 ng/ml FGF2 (Invitrogen). NPCs are maintained at high density, grown on PORN/Laminin-coated plates in NPC media and split approximately 1:4 every week with Accutase (Millipore). For neural differentiations, NPCs were dissociated with Accutase and plated at low density in neural differentiation media (DMEM/F12-Glutamax, 1×N2, 1×B27-RA, 20 ng/ml BDNF (Peprotech), 20 ng/ml GDNF (Peprotech), 1 mm dibutyrl-cyclicAMP (Sigma), 200 nM ascorbic acid (Sigma) onto PORN/Laminin-coated plates. Assays for neuronal connectivity, neurite outgrowth, synaptic protein expression, synaptic density, electrophysiology, spontaneous calcium transient imaging and gene expression were used to compare control and SCZD hiPSC neurons. Additional methods are found in S.I.

Description of Schizophrenic Patients

All patient samples were obtained from the Coriell collection. Patients were selected based on the high likelihood of a genetic component to disease. Patient 1 (GM02038, male, 22 years of age, Caucasian) was diagnosed with SCZD at six years of age and committed suicide at 22 years of age. Patient 2 (GM01792, male, 26 years of age, Jewish Caucasian) displayed episodes of agitation, delusions of persecution, and fear of assassination. His sister, patient 3 (GM01835, female, 27 years of age, Jewish Caucasian) had a history of schizoaffective disorder and drug abuse. Patient 4 (GM02497, male, 23 years of age, Jewish Caucasian) was diagnosed with SCZD at age 15 and showed symptoms including paralogical thinking, affective shielding, splitting of affect from content, and suspiciousness. His sister, patient 5 (GM02503, female, 27 years of age, Jewish Caucasian) was diagnosed with anorexia nervosa in adolescence and with schizoid personality disorder (SPD) as an adult. SPD has an increased prevalence in families with SCZD but is a milder diagnosis characterized not by psychosis but rather by a lack of interest in social relationships and emotional coldness (Association, A. P. Diagnostic and statistical manual of mental disorders: DSM-IV. 3rd ed., rev. edn, Vol. 4th ed. (American Psychiatric Press, 1994). Though Applicants show data from SPD patient 5 as an interesting point of comparison, we do not consider patient 5 to belong to either the “control” or “SCZD” groups.

Preliminary experiments were controlled using BJ fibroblasts from ATCC (CRL-2522). These fibroblasts were expanded from foreskin tissue of a newborn male. They are readily reprogrammed, low passage, karyotypically normal and extremely well-characterized primary fibroblast line cells. Age and ancestry matched controls were obtained from three Coriell collections: apparently healthy individuals with normal psychiatric evaluations, apparently healthy non-fetal tissue and gerontology research center cell cultures. hiPSCs were generated from GM02937 (male, 22 years of age), and GM03440 (male, 20 years of age), GM03651 (female, 25 years of age), GM04506 (female, 22 years of age), AG09319 (female, 24 years of age) and AG09429 (female, 25 years of age).

Generation of Lentivirus

Lentivirus was packaged in 293T HEK cells grown in 293T media (IMEM (Invitrogen), 10% FBS (Gemini), 1× Glutamax (Invitrogen)). 293T cells were transfected with Polyethylenimine (PEI) (Polysciences). Per 15-cm plate, the following solution was prepared, incubated for 5 minutes at room temperature and added drop-wise to plates: 12.2 μg lentiviral DNA, 8.1 μg MDL-gagpol, 3.1 μg Rev-RSV, 4.1 μg CMV-VSVG, 500 μl of IMDM and 110 μl PEI (1 μg/μl) and vortexed lightly. Medium was changed after three hours and the virus was harvested at 48 and 72 hours post transfection.

hiPSC Derivation

HFs were cultured on plates treated with 0.1% gelatin (in milliβQ water) for a minimum of 30 minutes and grown in HF media (DMEM (Invitrogen), 10% FBS (Gemini), 1× Glutamax (Invitrogen), 5 ng/ml FGF2 (Invitrogen)).

HFs were infected daily for five days with tetracycline-inducible lentiviruses expressing OCT4, SOX2, KLF4, cMYC and LIN28, driven by a sixth lentivirus expressing the reverse tetracycline transactivator (rtTA)⁷. Cells from a single well of a six-well dish were split onto a 10-cm plate containing 1 million mouse embryonic fibroblasts (mEFs). Cells were switched to HUES media (KO-DMEM (Invitrogen), 10% KO-Serum Replacement (Invitrogen), 10% Plasminate (Talecris), 1× Glutamax (Invitrogen), 1×NEAA (Invitrogen), 1×2βmercaptoethanol (Sigma) and 20 ng/ml FGF2 (Invitrogen)). 1 μg/ml Doxycycline (Sigma) was added to HUES media at for the first 21-28 days of reprogramming.

hiPSC colonies were manually picked and clonally plated onto 24-well mEF plates. hiPSC lines were either maintained on mEFs in HUES media or on Matrigel (BD) in TeSR media (Stemcell Technologies). At early passages, hiPSCs were split through manual passaging. At higher passages, hiPSC could be enzymatically passaged with Collagenase (1 mg/ml in DMEM) (Sigma). Cells were frozen in freezing media (DMEM, 10% FBS, 10% DMSO).

Karyotyping analysis was performed by Cell Line Genetics (Wisconsin, MD) or by Dr. Marie Dell'Aquila (UCSD).

Teratoma analysis was performed by injecting hiPSCs into the kidney capsules of isoflorane-anesthetized NOD-SCID mice. Teratomas were harvested eight weeks post-injection, paraffin-embedded and H&E stained.

hiPSC Differentiation to NPCs and Neurons

hiPSCs grown in HUES media on mEFs were incubated with Collagenase (1 mg/ml in DMEM) at 37° C. for one to two hours until colonies lifted from the plate and were transferred to a nonadherent plate (Corning). Embryoid Bodies (EBs) were grown in suspension in N2 media (DMEM/F12-Glutamax (Invitrogen), 1×N2 (Invitrogen)). After seven days, EBs were plated in N2 media with 1 μg/ml Laminin (Invitrogen) onto polyornithine (PORN)/Laminin-coated plates. Visible rosettes formed within one week and were manually dissected onto PORN/Laminin-coated plates. Rosettes were cultured in NPC media (DMEM/F12, 1×N2, 1×B27-RA (Invitrogen), 1 μg/ml Laminin and 20 ng/ml FGF2) and dissociated in TrypLE (Invitrogen) for three minutes at 37° C. NPCs are maintained at high density, grown on PORN/Laminin-coated plates in NPC media and split approximately 1:4 every week with Accutase (Millipore).

For neural differentiations, NPCs were dissociated with Accutase and plated in neural differentiation media (DMEM/F12, 1×N2, 1×B27-RA, 20 ng/ml BDNF (Peprotech), 20 ng/ml GDNF (Peprotech), 1 mm dibutyrl-cyclicAMP (Sigma), 200 nm ascorbic acid (Sigma) onto PORN/Laminin-coated plates. Density is critical and the following guidelines were used: two-well permanox slide, 80-100,000 cells/well; 24-well, 40-60,000 cells/well; six-well, 200,000 cells/well. hiPSC derived-neurons were differentiated for 1-3 months. Notably, synapse maturation occurs most robustly in vitro when hiPSC neurons are cocultured with wildtype human cerebellar astrocytes (Sciencell). 0.5% FBS was supplemented into neural differentiation media for all astrocyte coculture experiments.

It is difficult to maintain healthy neurons for three months of differentiation and some cultures invariably fail or become contaminated. When even one SCZD patient neural culture failed, the experiments were abandoned as all assays were conducted on neurons cultured in parallel. If, however, only a control neural culture failed, and at least three control samples remained, analysis was completed. For this reason, though patients are consistently numbered throughout the manuscript, controls are not, and are instead listed in numerical order (BJ, GM02937, GM03651, GM04506, AG09319, AG09429).

Antipsychotic drugs were added for the final three weeks of a three-month differentiation on astrocytes and for the final two weeks of a six-week differentiation on PORN/laminin alone. Drugs were resuspended in DMSO at the following concentrations: Clozapine (5 μM), Loxapine (10 μM), Olanzapine (1 μM), Risperidone (10 μM) and Thioridazine (5 μM).

Immunohistochemistry

Cells were fixed in 4% paraformaldehyde in PBS at 4° C. for 10 minutes. hiPSCs and NPCs were permeabilized at room temperature for 15 minutes in 1.0% Triton in PBS. All cells were blocked in 5% donkey serum with 0.1% Triton at room temperature for 30 minutes. The following primary antibodies and dilutions were used: mouse anti-Oct4 (Santa Cruz), 1:200; goat anti-Sox2 (Santa Cruz), 1:200; goat anti-Nanog (R&D), 1:200; mouse anti-Tra1-60 (Chemicon), 1:100; mouse anti-human Nestin (Chemicon), 1:200; rabbit anti-βIII-tubulin (Covance), 1:200; mouse anti-BIII-tubulin (Covance), 1:200; rabbit anti-cow-GFAP (Dako) 1:200; mouse anti-MAP2ab (Sigma), 1:200; rabbit anti-synapsin (Synaptic Systems), 1:500; mouse anti-PSD95 (UCDavis/NIH Neuromab), 1:500; rabbit anti-PSD95 (Invitrogen), 1:200 rabbit-anti-vGlut1 (Synaptic; Systems), 1:500; rabbit anti-Gephyrin, (Synaptic Systems), 1:500; mouse anti-vGat (Synaptic Systems), 1:500; rabbit anti-vGat (Synaptic Systems), 1:500; rabbit anti-GluR1 (Oncogene), 1:100; rabbit anti-GABA (Sigma), 1:200; rabbit anti-GAD67 (Sigma), 1:200.

Secondary antibodies were Alexa donkey 488, 555 and 647 anti-rabbit (Invitrogen), Alexa donkey 488 and 555 anti-mouse (Invitrogen), and Alexa donkey 488, 555, 568 and 594 anti-goat (Invitrogen); all were used at 1:300. To visualize nuclei, slides were stained with 0.5 μg/ml DAPI (4′,6-diamidino-2-phenylindole) and then mounted with Vectashield. Images were acquired using a Bio-Rad confocal microscope.

FACS

For sorting of dissociated hiPSC-derived neurons, cultures were dissociated in trypsin for 5 minutes, washed in DMEM, centrifuged at 500×g and resuspended in PBS. Cells were fixed in 4% paraformaldehyde in PBS at 4° C. for 10 minutes. Cells were washed in PBS and aliquoted into 96-well conical plates. Cells were blocked in 5% donkey serum with 0.1% saponin at room temperature for 30 minutes. The following primary antibodies and dilutions were used for one hour at room temperature: rabbit anti-βIII-tubulin (Sigma), 1:200; mouse anti-MAP2a+b (Sigma), 1:100. Cells were washed and then incubated with secondary antibodies at 1:200 for 30 minutes at room temperature: Alexa donkey 647 anti-rabbit (Invitrogen), and Alexa donkey 488 anti-mouse (Invitrogen). Cells were washed three times in PBS and stained with 0.5 μm/ml DAPI (4′,6-diamidino-2-phenylindole). Cells were resuspended in PBS with 5% donkey serum and 0.1% detergent saponin. The homogeneous solution was filtered through a 250-μM nylon sieve and run in a BD FACS Caliber. Data were analyzed using FloJo.

Rabies Virus Trans-Neuronal Tracing

Rabies virus trans-neuronal tracing was performed on three-month-old hiPSC neurons cocultured with wildtype human astrocytes (Sciencell) on acid-etched glass coverslips and then transduced with LV-SYNP-HTG or LV-SYNP-HT. Cultures were transduced with Rabies-ENVAΔG-RFP after at least a week to allow expression of ENVA and rabies G. Either 5, 7 or 10 days later, hiPSC neurons were either dissociated with accutase for FACS analysis of fixed with 4% paraformaldehyde in PBS for fluorescent microscopy.

Neurite Analysis

Neurite analysis was performed on three-month-old hiPSC neurons cocultured with wildtype human astrocytes (Sciencell) on acid-etched glass. Low titer transduction of a lentivirus driving expression of GFP from the SYN promoter (LV-SYNP-GFP) occurred at least 7 days prior to assay. LV-SYNP-GFP was used to image and count branching neurites from single neurons (FIG. 3A). The number of neurites extending from the soma of 691 single LV-SYNP-GFP-labeled neurons was determined by a blinded count.

Synaptic Protein Staining Analysis

Synaptic protein staining was performed on three-month-old hiPSC neurons cocultured with wildtype human astrocytes (Sciencell) on acid-etched glass. To calculate ratios of MAP2AB-positive dendrites and synaptic proteins, confocal images were taken at 630× magnification and 4× zoom. Using NIH ImageJ, images were thresholded and the integrated pixel density was determined for each image. Integrated pixel density measurement is the product of area (measured in square pixels) and mean gray value (the sum of the gray values of all the pixels in the selection divided by the number of pixels).

Synapse Density

Manual counts of synaptic density were done in three steps using NIH ImageJ. First, the colocalization plugin was used to identify colocalization of VGLUT1 and PSD95. Second, the particle analysis function was used to restrict size 50-infinity. Third, dendrites were traced using the NeuronJ plugin. The mask generated by particle analysis was overlayed on the trace generated by NeuronJ and synapses were manually counted.

Electrophysiology

Whole-cell perforated patch recordings were performed on SCZD (n=30) and control (n=20) three-month-old hiPSC neurons cocultured with wildtype human astrocytes (Sciencell) on acid-etched coverslips and typically transduced with LV-SYNP-GFP. The recording micropipettes (tip resistance 3-6 MÙ) were tip-filled with internal solution composed of 115 mM K-gluconate, 4 mM NaCl, 1.5 mM MgCl2, 20 mM HEPES, and 0.5 mM EGTA (pH 7.4) and then back-filled with the same internal solution containing 200 μg/ml amphotericinB (Calbiochem). Recordings were made using Axopatch 200B amplifier (Axon Instruments). Signals were sampled and filtered at 10 kHz and 2 kHz, respectively. The whole-cell capacitance was fully compensated, whereas the series resistance was uncompensated but monitored during the experiment by the amplitude of the capacitive current in response to a 5 mV pulse. The bath was constantly perfused with fresh HEPES-buffered saline composed of 115 mM NaCl, 2 mM KCl, 10 mM HEPES, 3 mM CaCl₂, 10 mM glucose and 1.5 mM MgCl₂ (pH 7.4). For voltage-clamp recordings, cells were clamped at −60 to −80 mV; Na+ currents and K+ currents were stimulated by voltage step depolarizations. Command voltage varied from −50 to +20 mV in 10 mV increments. For current-clamp recordings, induced action potentials were stimulated with current steps from −0.2 to +0.5 nA. All recordings were performed at room temperature.

Spontaneous Calcium Transients

Culture media was removed and hiPSC cultures were incubated with 0.4 μM Fluo-4AM (Molecular Probes) and 0.02% Pluronic F-127 detergent in Krebs HEPES Buffer (KHB) (10 mM HEPES, 4.2 mM NaHCO₃, 10 mM dextrose, 1.18 mM MgSO₄.2H₂O, 1.18 mM KH₂PO₄, 4.69 mM KCl, 118 mM NaCl, 1.29 mM CaCl₂; pH 7.3) for one hour at room temperature. Cells were washed with KHB buffer, incubated for two minutes with Hoechst dye diluted 1:1000 in KHB, and allowed to incubate for an additional 15 minutes in KHB to equilibrate intracellular dye concentration. Time lapse image sequences (100× magnification) were acquired at 28 Hz using a Hamamatsu ORCA-ER digital camera with a 488 nm (FITC) filter on an Olympus IZ81 inverted fluorescence confocal microscope. Images were acquired with MetaMorph.

In total, eight independent neural differentiations were tested per patient, 210 movies of spontaneous calcium transients (110 control and 100 schizophrenic) were generated and 2,676 ROIs (1,158 control and 1,518 schizophrenic ROIs) were analyzed. Up to four 90-second videos of Fluo-4AM fluorescence were recorded per neural differentiation per patient with a spinning disc confocal microscope at 28 frames per second (Supplementary FIG. 2A). Using ImageJ software, regions of interest (ROIs) can be manually selected and the mean pixel intensity of each ROI can be followed over time, generating time trace data for each ROI. The data were analyzed in Matlab where background subtraction was performed by normalizing traces among traces of the sample, and spike events were identified based on the slope and amplitude of the time trace.

The amplitude of spontaneous calcium transients was calculated by measuring the change in total pixel intensity for each normalized calcium transient trace. The rate was determined by dividing the total number of spontaneous calcium transients for any ROI by the total length of the movie (90 seconds). The synchronicity of spontaneous calcium transients was determined by two independent calculations. First, to determine the percentage synchronicity per calcium transient, the total number of synchronized calcium transients, defined as three or more simultaneous peaks, was divided by the total number of spontaneous calcium transients identified. Second, to calculate the maximum percentage synchronicity, the maximum number of ROIs involved in a single synchronized event was divided by the total number of ROIs identified.

CNV Analysis

Cells were lysed in DNA Lysis solution (100 mM Tris, pH 8.5, 5 mM EDTA, 200 mM NaCl, 0.2% (w/v) sarcosyl, and 100 μg/ml fresh proteinase K) overnight at 50° C. DNA was precipitated by the addition of an equal volume of NaCl-ethanol mixture (150 μl of 5 M NaCl in 10 ml cold 95% ethanol) and then washed three times in 70% ethanol prior to resuspension in water with RNAseA overnight at 4° C.

Genome Scans were performed using NimbleGen HD2 arrays (NimbleGen Systems Inc) according the to the manufacturer's instructions using a standard reference genome SKN1. NimbleGen HD2 dual-color intensity data were normalized in a two-step process: first, a ‘spatial’ normalization of probes was performed to adjust for regional differences in intensities across the surface of the array, and second, the Cy5 and Cy3 intensities were adjusted to a fitting curve by invariant set normalization, preserving the variability in the data. The log 2 ratio for each probe was then estimated using the geometric mean of normalized and raw intensity data (McCarthy, S. E. et al., Nature Genetics 41:1223-1227).

CNV analysis was completed to identify deletions and duplications present within the patients. By using a virtual “genotyping” step whereby individual CNV segment probe ratios were converted into z-scores, a distribution of median Z-scores were generated, outliers of which were considered to be true CNVs. In doing so, Applicants better filtered out common artifacts and false positive CNVs and generated a list of CNVs unbiased by previous genetic studies of schizophrenia.

Patient fibroblasts were used for CNV analysis. Lymphocytes were available for patient 4 and his parents, allowing us to validate the CNVs identified for patient 4 and also determine the parent of origin for each mutation; many were inherited from the unaffected mother (Table 8)

Gene Expression Analysis

Cells were lysed in RNA BEE (Tel-test, Inc). RNA was chloroform extracted, pelleted with isopropanol, washed with 70% ethanol and resuspended in water. RNA was treated with RQ1 RNAse-free DNAse (Promega) for 30 minutes at 37° C. and then the reaction was inactivated by incubation with EGTA Stop buffer at 65° C. for 10 minutes.

For gene expression arrays, three independent neural differentiations for each of the 4 schizophrenic patients, as well as 4 control subjects, were compared using Affymetrix Human 1.0ST arrays as specified by the manufacturer.

Gene expression array analysis was completed using Partek software. Pathway analysis was performed using Metacore GeneGo.

For qPCR, cDNA was synthesized using Superscript III at 50° C. for one to two hours, inactivated for 15 minutes at 70° C. and then treated with RNAaseH for 15 minutes at 37° C., inactivated with EDTA and heated to 70° C. for 15 minutes. qPCR was performed using SybrGreen. Primers used are listed in Table 8.

Statistical Analysis

Statistical analysis was completed using JMP software. Data was transformed into a normal distribution using a box-cox transformation. The Shapiro-Wilk W test was performed to ensure a normal distribution. Means were compared within diagnosis by One way analysis using both Student's T test and Tukey Kramer HSD. Finally, a nested analysis of values for individual patients and controls was performed using standard least squares analysis comparing means for all pairs using both Student's T test and Tukey Kramer HSD.

B. Results

Four SCZD patients were selected: patient 1, diagnosed at six years of age, had childhood-onset SCZD; patients 2, 3 and 4 were from families in which all offspring and one parent were affected with psychiatric disease. Primary human fibroblasts (HFs) were reprogrammed using inducible lentiviruses⁷. Control and SCZD hiPSCs expressed endogenous pluripotency genes, repressed viral genes and were indistinguishable in assays for self-renewal and pluripotency (FIG. 1). SCZD hiPSCs had no apparent defects in generating neural progenitor cells (NPCs) or neurons (FIG. 1; FIG. 5). Most hiPSC neurons were presumably glutamatergic and expressed VGLUT1 (FIG. 11A). Approximately 30% of neurons were GAD67-positive (GABAergic) (FIG. 11C,D) whereas less than 10% of neurons were tyrosine hydroxylase (TH)-positive (dopaminergic) (FIG. 10).

Neuronal connectivity was assayed using trans-neuronal spread of rabies; in vivo, rabies transmission occurs via synaptic contacts and is strongly correlated with synaptic input strength⁸. Primary infection was restricted by replacing the rabies coat protein with envelope A (ENVA), which infects only via the avian tumor virus A (TVA) receptor; viral spread was limited to monosynaptically connected neurons by deleting the rabies glycoprotein gene (AG)⁹. Neurons were first transduced with a lentivirus expressing Histone 2B (H2B)-green fluorescent protein (GFP) fusion protein, TVA and G from the synapsin (SYN) promoter (LV-SYNP-HTG). One week later, neurons were transduced with modified rabies (Rabies-ENVAΔG-RFP). Primary infected cells were positive for both H2BGFP and RFP; neurons monosynaptically connected to primary cells were GFP-negative but RFP-positive (FIG. 7A). Transduction with Rabies-ENVAΔG-RFP alone resulted in no RFP-positive cells, whereas transduction with Rabies-ENVAΔG-RFP following lentiviral transduction without rabies glycoprotein (SYNP-HT) led to only single GFP⁺ RFP⁺ cells, indicating that in vitro rabies infection and spread are dependent on TVA expression and G trans-complementation, respectively (FIG. 7C,D).

There was decreased neuronal connectivity in SCZD hiPSC neurons (FIG. 2; FIG. 8B,C; FIG. 8,5). FACS analysis confirmed differences in neuronal connectivity and demonstrated that comparable numbers of βIII-tubulin-positive neurons were labeled with LV-SYNP-HTG. Though the mechanism of rabies trans-neuronal tracing is not fully understood, the presynaptic protein NCAM has been implicated¹⁰; NCAM expression is decreased in SCZD hiPSC neurons (Table 5). Rabies trans-neuronal tracing occurs in functionally immature hiPSC neurons (FIG. 7E) and in the presence of the voltage-gated sodium channel blocker tetrodotoxin (TTX) (1 μM), depolarizing KCl (50 mM) or the calcium channel blocker ryanodine (10 μM) (FIG. 7F). Decreased trans-neuronal tracing is evidence of decreased neuronal connectivity, but not necessarily decreased synaptic function, in SCZD hiPSC neurons.

Applicants tested the ability of five antipsychotic drugs to improve neuronal connectivity in vitro. Clozapine, Loxapine, Olanzapine, Risperidone and Thioridazine were administered for the final three weeks of neuronal differentiation. Only Loxapine significantly increased neuronal connectivity in hiPSC neurons from all patients (FIG. 2B; FIG. 8). Optimization of the concentration and timing of drug administration may improve the effects of the other antipsychotic medications.

Reduced dendritic arborization has been observed in postmortem SCZD brains¹¹ and in animal models¹². SCZD hiPSC neurons show a decrease in the number of neurites (FIG. 3A; FIG. 12A,B). Synaptic genes are associated with SCZD¹³ (FIG. 12D) and impaired synaptic maturation occurs in a number of mouse models¹². hiPSC neurons express dense puncta of synaptic markers that co-stain for both pre- and post-synaptic markers (FIG. 11A,B). While Applicants observed decreased PSD95 protein expression relative to MAP2AB in SCZD hiPSC neurons (FIG. 3B; FIG. 12H), the levels of SYN, VGLUT1, GLUR1, VGAT and GEPH were unaffected (FIG. 12E-I). Decreased PSD95 synaptic density in SCZD hiPSC neurons failed to reach statistical significance (FIG. 3C; FIG. 12C).

Applicants used electrophysiology and calcium transient imaging to measure spontaneous neuronal activity (FIG. 3D-K; FIG. 13). SCZD hiPSC neurons showed normal transient inward sodium currents and sustained outward potassium currents in response to membrane depolarizations (FIG. 3D), action potentials to somatic current injections, (FIG. 3E), excitatory postsynaptic currents (EPSCs) (FIG. 3F) and inhibitory postsynaptic currents (IPSCs) (FIG. 3G). The amplitude and rate of spontaneous calcium transients were unaffected (FIG. 3H-J; FIG. 13A-D) and there was no difference in synchronicity of spontaneous calcium transients (FIG. 3K; FIG. 13E-G).

Increased NRG1 expression has been observed in postmortem SCZD brain tissue¹³. NRG1 expression was increased in SCZD hiPSC neurons (FIG. 4D-F) but not SCZD fibroblasts (HF), hiPSCs or NPCs (FIG. 4E), demonstrating the importance of studying gene expression changes in the cell type relevant to disease. In all, 596 unique genes (271 upregulated and 325 downregulated) showed greater than 1.30-fold-expression changes between SCZD and control hiPSC neurons (p<0.05) (FIG. 14A,B; Table 5). Of these genes, 13% (74) have published associations with SCZD and 16% (96) have been linked to SCZD by postmortem gene expression profiles available through the Stanley Medical Research Institute¹⁴ (Table 5); in total 25% (149) of the differentially expressed genes have been previously implicated in SCZD. Gene ontology (GO) analysis identified significant perturbations of glutamate, cAMP and WNT signaling (FIG. 4A-C; Table 6), pathways required for activity-dependent refinement of synaptic connections and long-term potentiation¹⁵⁻¹⁷. Sixteen of 17 candidate genes from these families were validated by qPCR (Table 4; FIG. 4F; FIG. 14C).

Copy number variants (CNVs) are rare, highly penetrant structural disruptions. SCZD patients have a 1.15-fold increase in CNV burden, but how this translates into illness is unknown. Patient 4 had four CNVs involving genes previously associated with SCZD or bipolar disorder (BD)^(13,18,19); of these, neuronal expression of NRG3 and GALNT11, but not of CYP2C19 or GABARB2/GABARA6 was affected (FIG. 15, Table 7). A second analysis of CNVs unbiased by previous GWAS studies identified 42 genes affected by CNVs in the four SCZD patients (Table 7). Though twelve of these genes showed altered neuronal expression consistent with genotype (p<0.05), most changes were extremely small and only three (CSMD1, MYH1, MYH4) showed >1.3-fold effects (Table 7). Well-established SCZD CNVs occur at 1q21.1, 15q11.2, 15q13.3, 16p11.2 and 22q11.2,^(13,18,19), but the relevant genes remain unidentified. The patients had no evidence of CNVs at these regions, and gene expression of the best candidate genes in each region, such as GJA8 (1q21.1), CYFIP1 (15q11.1), CHRFAM7A (15q13.3), PRODH (22q11.2), COMT (22q11.2) and ZDHHC8 (22q11.2)¹⁸′²⁰, was not affected in the SCZD hiPSC neurons (Table 8).

Consistent with published reports, Loxapine increased NRG1 expression in neurons²¹. Loxapine also increased expression of several glutamate receptors. ADCY8, PRKCA, WNT7A and TCF4 also showed ameliorated expression with Loxapine (FIG. 4F; FIG. 14C).

C. Discussion

SCZD hiPSC neurons from heterogeneous patients had similar deficits, replicating some but not all aspects of the cellular and molecular phenotypes observed in post-mortem human studies and animal models (Table 3). Applicants observed decreased neuronal connectivity in SCZD hiPSC neurons, but not defects in synaptic function; this may reflect technical limitations of the synaptic activity assays. Due to the heterogeneity of the patient cohort and small sample size, the findings might not generalize to all subtypes of SCZD and the microarray comparisons of SCZD and control hiPSC neurons are necessarily preliminary. Gene expression studies of hiPSC neurons permit straightforward comparisons of antipsychotic treatments on live, genetically identical neurons from patients with known clinical treatment outcomes, eliminating many confounding variables of postmortem analysis such as treatment history, drug or alcohol abuse, and cause of death. For example, though Loxapine is characterized as a high affinity antagonist of serotonin 5-HT₂ receptors and dopamine D₁, D₂ and D₄ receptors²², treatment of SCZD hiPSC neurons resulted in altered gene expression and increased neuronal connectivity.

Of the 596 unique genes differentially expressed in the SCZD hiPSC neurons (>1.30-fold, p<0.05), 25% have been previously implicated in SCZD (Table 5). While the gene expression profiles of SCZD hiPSC neurons confirm and extend the major hypotheses generated by pharmacological and GWAS studies of SCZD, they also identify some pathways not before linked to SCZD, such as NOTCH signaling, SLIT/ROBO axon guidance, EFNA mediated axon growth, cell adhesion and transcriptional silencing (Table 6). Many of the genes most affected in SCZD hiPSC neurons belong to pathways previously associated with SCZD, though they have not yet been singled out as SCZD genes. For example, while PDE4B is a well-characterized SCZD gene, Applicants observed significant misexpression of PDE1C, PDE3A, PDE4D, PDE4DIP, PDE7B, ADCY7 and ADCY8. Additionally, though some key SCZD/BD genes, including NRG1 and ANK3, were misexpressed in all of the SCZD hiPSC neurons, many others, including ZNF804A, GABRB1, ERBB4, DISC1 and PDE4B, were aberrantly expressed in some but not all patients. The data support the “watershed model”²³ of SCZD whereby many different combinations of gene misfunction may disrupt the key pathways affected in SCZD. Applicants predict that, as the number of SCZD cases studied using hiPSC neurons increases, a diminishing number of genes will be consistently affected across the growing patient cohort; instead, evidence will accumulate that a handful of essential pathways can be disrupted in diverse ways to result in SCZD.

IV. References

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V. Tables and Supplementary Tables

TABLE 1 Genes identified by microarray analysis as showing the greatest fold-change in expression in schizophrenic hiPSC-derived neurons. Fold-Change Gene Symbol RefSeq (SCZD vs Control) P-value PMP2 NM_002677 −10.3717 0.0203837 FLJ16686 AK304357 −5.6709 0.0362611 CHST9 NM_031422 −5.56568 0.000386164 AQP4 NM_001650 −4.83804 0.0217381 PRSS35 NM_153362 −4.57339 0.0391452 HEY2 NM_012259 −4.40862 0.00365555 GRIK1 NM_175611 −3.89439 0.0039328 CYYR1 NM_052954 −3.5739 0.00808509 PGM5 NM_021965 −3.56835 0.00378535 GFAP NM_002055 −3.49626 0.0139662 ASS1 NM_000050 3.97469 0.0106259 FAT4 NM_024582 4.38381 0.00513286 ZMAT4 NM_024645 4.43352 0.00910539 VGLL3 NM_016206 4.55739 0.00346015 IFITM1 NM_003641 4.84429 0.0275079 SNORD113-3 NR_003231 5.03561 0.0434844 SNORD114-3 NR_003195 5.1557 0.0471367 SERPINI1 NM_001122752 5.61545 0.00474614 PAX3 NM_181458 6.13902 0.00580902 ZIC1 NM_003412 9.43152 0.00103707

TABLE 2 Microarray and qPCR validation of changes in expression of glutamate receptor, cAMP and Wnt genes in schizophrenic hiPSC-derived neurons. Microarray Gene Expression qPCR Gene Expression Fold-Change p-value Fold-Change p-value Gene Symbol RefSeq (SCZD vs CNTL) (Diagnosis) (SCZD vs CNTL) (Diagnosis) GRIK1 NM_175611 −3.89 0.0039 nd nd GRIK4 NM_014619 −1.90 0.0402 nd nd GRIN1 NM_007327 1.16 0.0448 nd nd GRIN2A NM_001134407 −1.72 0.0421 −4.26 <0.0001 GRM1 NM_001114329 1.27 0.0052 nd nd GRM7 NM_181874 −1.48 0.0190 −2.26 <0.0001 DRD2 NM_000795 1.13 0.0091 nd nd GNG2 NM_053064 1.20 0.0254 nd nd ADCY8 NM_001115 −2.03 0.0496 −4.90 <0.0001 ITPR2 NM_002223 −1.72 0.0081 nd nd PDE1C NM_005020 2.96 0.0414 nd nd PDE3A NM_000921 1.25 0.0452 1.47 0.0016 PDE4D NM_001104631 1.84 0.0001 2.18 <0.0001 PDE4DIP NM_022359 1.48 0.0318 1.30 0.0076 PDE6A NM_000440 −1.10 0.0329 nd nd PDE7B NM_018945 3.16 0.0114 3.60 <0.0001 PDE8A NM_002605 1.19 0.0186 −2.26 <0.0001 PDE10A NM_006661 1.33 0.0330 −1.46 0.1301 PRKAR2A NM_004157 1.25 0.0391 nd nd PRKCA NM_002737 −2.41 0.0219 −4.64 <0.0001 PIP5K1B NM_003558 2.03 0.0252 nd nd PIK3R3 NM_003629 1.40 0.0329 nd nd RAP1A NM_001010935 1.19 0.0455 −1.19 0.3198 RAP2A NM_021033 −1.41 0.0066 −2.15 <0.0001 WNT2B NM_024494 1.41 0.0308 nd nd WNT3 NM_030753 1.31 0.0077 nd nd WNT7A NM_004625 −1.62 0.0120 −2.18 <0.0001 WNT7B NM_058238 1.14 0.0069 nd nd LRP5 NM_002335 −1.29 0.0135 −1.32 0.1920 AXIN2 NM_004655 1.39 0.0191 2.93 0.0096 TCF4 NM_001083962 1.33 0.0148 nd nd LEF1 NM_016269 2.07 0.0496 2.10 <0.0001

TABLE 3 Summary of positive and negative findings of cellular phenotypes in SCZD hiPSC neurons. Predicted Aspects of SCZD Cellular Positive Findings in Negative Findings in SCZD Pathology SCZD hiPSC Neurons hiPSC Neurons Reduced neuronal Decreased rabies — connectivity trans-neuronal tracing Reduced neurite Reduced neurite — outgrowth outgrowth Reduced synaptic Decreased PSD95 No change in vGLUT1, protein levels GLUR1, VGAT or GEPH Reduced synaptic — Not observed density Decreased synaptic — No change in EPSCs, iPSCs, function or the amplitude, frequency or spontaneity of spon- taneous calcium transients Antipsychotic Improved neuronal No improvement with treatment connectivity with Clozapine (5 μM), Loxapine (10 μM) Olanzapine (1 μM), Risperidone (10 μM) and Thioridazine (5 μM)

TABLE 4 Microarray and qPCR validation of changes in expression of glutamate receptor, cAMP and Wnt genes in SCZD hiPSC neurons. Microarray Gene Expression qPCR Gene Expression Fold-Change Fold-Change Gene Symbol RefSeq (SCZD vs CNTL) p-value (SCZD vs CNTL) p-value GRIK1 NM_175611 −3.9 0.0039 −6.8 <0.0001 GRIK4 NM_014619 −1.9 0.0402 nd nd GRIN2A NM_001134407 −1.7 0.0421 −4.3 <0.0001 GRM1 NM_001114329 1.3 0.0052 nd nd GRM7 NM_181874 −1.5 0.0190 −2.3 <0.0001 NRG1 NM_013958 1.7 0.0038 2.8 <0.0001 ADCY7 NM_001114 −1.3 0.0052 nd nd ADCY8 NM_001115 −2.0 0.0496 −4.9 <0.0001 ITPR2 NM_002223 −1.7 0.0081 nd nd PDE10A NM_006661 1.3 0.0330 −1.5 0.1301 PDE1C NM_005020 3.0 0.0414 nd nd PDE3A NM_000921 1.3 0.0452 1.5 0.0016 PDE4D NM_001104631 1.8 0.0001 2.2 <0.0001 PDE4DIP NM_022359 1.5 0.0318 1.3 0.0076 PDE7B NM_018945 3.2 0.0114 3.6 <0.0001 PRKAR2A NM_004157 1.3 0.0391 nd nd PRKCA NM_002737 −2.4 0.0219 −4.6 <0.0001 PRKG1 NM_001098512 −1.4 0.0112 nd nd PIP5K1B NM_003558 2.0 0.0252 nd nd PTPRE NM_006504 −1.7 0.0213 nd nd PTPRR NM_002849 1.3 0.0487 nd nd PIK3R3 NM_003629 1.4 0.0329 nd nd RAP2A NM_021033 −1.4 0.0066 −2.1 <0.0001 WNT2B NM_024494 1.4 0.0308 nd nd WNT3 NM_030753 1.3 0.0077 nd nd WNT7A NM_004625 −1.6 0.0120 −2.2 <0.0001 LRP5 NM_002335 −1.3 0.0135 −1.3 0.1920 AXIN2 NM_004655 1.4 0.0191 2.9 0.0096 TCF4 NM_001083962 1.3 0.0148 2.8 <0.0001 LEF1 NM_016269 2.1 0.0496 2.1 <0.0001

TABLE 5 Genes identified as significantly misexpressed (p < 0.05) with >1.30-fold change in schizophrenic hiPSC neurons relative to controls. Fold- Stanley Foundation SCZD Post-Mortem Microarray Change Gene Expression Studies Consistent with SCZD (SCZD Published hiPSC Neuron Gene Expression vs p- Associations with Sklar- Sklar- Gene Symbol RefSeq Control) value SCZD Altar-A Altar-C Bahn Dobrin Feinberg Kato A B PMP2 NM_002677 −10.372 0.020 FLJ16686 AK304357 −5.671 0.036 CHST9 NM_031422 −5.566 0.000 AQP4 NM_001650 −4.838 0.022 Muratake, 2005 - X X PMID: 16194264 PRSS35 NM_153362 −4.573 0.039 HEY2 NM_012259 −4.409 0.004 GRIK1 NM_175611 −3.894 0.004 Shibata, 2001 - PMID: 11702055 CYYR1 NM_052954 −3.574 0.008 PGM5 NM_021965 −3.568 0.001 GFAP NM_002055 −3.496 0.014 Jungerius, 2007 - PMID: 17893707 SPP1 NM_001040058 −3.423 0.038 Jungerius, 2007 - PMID: 17893707 SLC4A4 NM_001098484 −3.404 0.007 X X CATSPERB NM_024764 −3.279 0.038 PGM5P2 NR_002836 −3.145 0.002 CADPS2 NM_017954 −3.126 0.006 SPARCL1 NM_001128310 −3.021 0.026 Kahler, 2008 - PMID: 18384059 TSPAN12 NM_012338 −2.948 0.001 PGM5P2 NR_002836 −2.943 0.003 FAM189A2 NM_004816 −2.917 0.007 X C1orf61 NM_006365 −2.897 0.029 LRIG3 NM_153377 −2.835 0.009 SLC34A2 NM_006424 −2.572 0.005 ARAP2 NM_015230 −2.514 0.001 X KLHDC8A NM_018203 −2.494 0.016 ADAMTS15 NM_139055 −2.494 0.014 PTCH1 NM_001083603 −2.420 0.045 C21orf63 NM_058187 −2.412 0.025 PRKCA NM_002737 −2.407 0.022 Carroll, 2009 - PMID: 19786960 LRAT NM_004744 −2.378 0.041 RASGRP1 NM_005739 −2.355 0.017 SOX6 NM_017508 −2.344 0.025 MFSD2 NM_001136493 −2.343 0.008 ACTN2 NM_001103 −2.325 0.002 KCNJ16 NM_170742 −2.269 0.006 SH3GL2 NM_003026 −2.266 0.009 Martins-de-Souza, 2009 - PMID: 19165527 SLC44A5 NM_152697 −2.254 0.006 ASTN1 NM_004319 −2.245 0.011 Kahler, 2008 - PMID: 18384059 KCNJ10 NM_002241 −2.236 0.014 Shen, 2010 - PMID: 20933057 GALNT13 NM_052917 −2.185 0.013 ASCL1 NM_004316 −2.170 0.010 Ide, 2005 - PMID: X 16021468 ITGA6 NM_000210 −2.156 0.010 ADHFE1 NM_144650 −2.139 0.013 SDC3 NM_014654 −2.135 0.036 GPT2 NM_133443 −2.131 0.014 SPON1 NM_006108 −2.112 0.040 X X ADCYAP1R1 NM_001118 −2.093 0.033 Hashimoto, 2007 - PMID: 17387318 SLC47A2 NM_152908 −2.086 0.010 HES6 NM_018645 −2.063 0.002 ADCY8 NM_001115 −2.025 0.050 IGSF9B NM_014987 −2.018 0.010 ALDH4A1 NM_003748 −2.010 0.019 TACR1 NM_001058 −2.010 0.038 Giegling, 2007 - PMID: 17443717 TC2N NM_001128596 −2.009 0.046 DBI NM_020548 −1.992 0.031 Niu, 2004 - PMID: 14755437 CD34 NM_001773 −1.984 0.022 EGF NM_001963 −1.981 0.021 Anttila, 2004 - PMID: 15129177 NTN1 NM_004822 −1.979 0.016 AQP7P1 NR_002817 −1.965 0.007 KCND3 NM_004980 −1.960 0.003 SERINC5 NM_178276 −1.959 0.009 SLC6A9 NM_201649 −1.950 0.023 Deng, 2008 - PMID: 18638388 C10orf72 NM_001031746 −1.950 0.031 DLGAP1 NM_004746 −1.941 0.021 Aoyama, 2003 - PMID: 12950712 RGMA NM_020211 −1.926 0.025 DLL1 NM_005618 −1.924 0.034 AQP7P1 NR_002817 −1.922 0.007 AQP7P1 NR_002817 −1.912 0.005 AQP7P1 NR_002817 −1.911 0.006 GRIK4 NM_014619 −1.904 0.040 Betcheva, 2009 - PMID: 19158809 NOTCH1 NM_017617 −1.903 0.014 Jungerius, 2007 - PMID: 17893707 HEPACAM NM_152722 −1.897 0.001 PLEKHB1 NM_021200 −1.896 0.020 ARHGEF4 NM_032995 −1.894 0.003 MAN1C1 NM_020379 −1.884 0.003 C4A NM_007293 −1.881 0.001 Rudduck, 1985 - X X PMID: 3875548 LOC283174 NR_024344 −1.876 0.007 PRDM8 NM_020226 −1.876 0.001 ITGA7 NM_001144996 −1.868 0.035 IGSF11 NM_001015887 −1.867 0.023 PFKFB3 NM_004566 −1.860 0.031 SLC38A3 NM_006841 −1.845 0.015 SGEF NM_015595 −1.842 0.009 LYPD6 NM_194317 −1.815 0.005 STAC NM_003149 −1.814 0.014 VWA5A NM_001130142 −1.814 0.007 S100A16 NM_080388 −1.810 0.001 IGSF9B NM_014987 −1.810 0.006 NKX6-1 NM_006168 −1.807 0.002 DDIT4L NM_145244 −1.792 0.001 MGST1 NM_145792 −1.791 0.019 ALDH1L1 NM_012190 −1.782 0.000 Kurian, 2011 - X X X PMID: 19935739 RNF148 NM_198085 −1.773 0.021 ATP1B2 NM_001678 −1.770 0.021 LPAR6 NM_005767 −1.766 0.025 X MEGF10 NM_032446 −1.765 0.024 Chen, 2008 - PMID: 18179784 SLC39A12 NM_001145195 −1.758 0.004 ALDOC NM_005165 −1.757 0.040 Martins-de-Souza, 2008 - PMID: 19110265 ANKFN1 NM_153228 −1.754 0.042 RNF133 NM_139175 −1.754 0.044 NOG NM_005450 −1.751 0.003 LRRCC1 NM_033402 −1.751 0.006 ACSBG1 NM_015162 −1.746 0.012 X WBSCR17 NM_022479 −1.746 0.027 ITGA3 NM_002204 −1.740 0.017 Kahler, 2008 - PMID: 18384059 PSRC1 NM_001032290 −1.738 0.002 X X ROBO2 NM_002942 −1.737 0.028 CCDC144A NM_014695 −1.736 0.026 ZBTB16 NM_006006 −1.735 0.002 X EFHD1 NM_025202 −1.732 0.028 X GRIN2A NM_001134407 −1.725 0.042 Itokawa, 2003 - PMID: 12724619 SOX2 NM_003106 −1.720 0.048 ITPR2 NM_002223 −1.720 0.008 X X NCAM1 NM_181351 −1.714 0.046 Atz, 2007 - PMID: X 17413444 SCARA3 NM_016240 −1.711 0.022 RAB31 NM_006868 −1.711 0.014 X X X SAMD4A NM_015589 −1.703 0.018 ZDHHC14 NM_024630 −1.702 0.008 PTPRE NM_006504 −1.702 0.021 S1PR1 NM_001400 −1.701 0.044 X SLC35D2 NM_007001 −1.700 0.037 LAMA5 NM_005560 −1.692 0.001 C4orf22 BC034296 −1.691 0.033 FAM181B NM_175885 −1.690 0.003 CNKSR3 NM_173515 −1.688 0.007 X SLC30A10 NM_018713 −1.687 0.028 C18orf16 AK055069 −1.684 0.012 KCNA4 NM_002233 −1.681 0.004 CSPG5 NM_006574 −1.678 0.046 So, 2009 - PMID: X 19367581 SLC12A4 NM_005072 −1.673 0.005 HNMT NM_006895 −1.672 0.001 Yan, 2000 - PMID: 10898922 CAV2 NM_001233 −1.662 0.032 EDNRB NM_001122659 −1.661 0.030 X UCP2 NM_003355 −1.660 0.000 Yasuno, 2006 - PMID: 17066476 CTD- NR_004846 −1.656 0.028 2514C3.1 PRCP NM_199418 −1.653 0.000 CYTSB NM_001033553 −1.651 0.050 SYNM NM_145728 −1.651 0.006 NEXN NM_144573 −1.649 0.014 NAT8L NM_178557 −1.645 0.003 LIX1 NM_153234 −1.642 0.016 TMEM132A NM_017870 −1.641 0.010 LRP1B NM_018557 −1.636 0.041 TLE3 NM_005078 −1.636 0.001 ITGB4 NM_000213 −1.635 0.041 X X SEMA5B NM_001031702 −1.630 0.043 CCDC144A NM_014695 −1.627 0.022 WNT7A NM_004625 −1.623 0.012 CELSR2 NM_001408 −1.622 0.035 X TPST1 NM_003596 −1.617 0.037 UNQ9374 AY358216 −1.615 0.012 AK3L1 NM_001005353 −1.607 0.011 ADRA1A NM_000680 −1.603 0.039 Bolonna, 2000 - PMID: 10696813 FMNL2 NM_052905 −1.597 0.013 X PRPH NM_006262 −1.590 0.024 ODZ4 NM_001098816 −1.584 0.019 FAM84B NM_174911 −1.579 0.024 ARNTL2 NM_020183 −1.578 0.040 Mansour, 2009 - PMID: 19839995 TYRO3 NM_006293 −1.578 0.003 X RNF220 NM_018150 −1.574 0.006 LAP3 NM_015907 −1.574 0.016 TRIM68 NM_018073 −1.569 0.043 COBL NM_015198 −1.567 0.015 SYTL2 NM_206927 −1.566 0.021 VAMP1 NM_199245 −1.563 0.004 X RXRG NM_006917 −1.563 0.025 CD9 NM_001769 −1.562 0.041 X SOCS2 NM_003877 −1.562 0.038 KAT2B NM_003884 −1.561 0.024 X MARCH3 NM_178450 −1.553 0.023 PPP2R2B NM_004576 −1.549 0.041 Chen, 2005 - X PMID: 16054804 TAAR3 BC095548 −1.548 0.004 DNHD1 NM_144666 −1.547 0.049 ABCD2 NM_005164 −1.546 0.041 PRAGMIN NM_001080826 −1.542 0.017 B4GALT5 NM_004776 −1.541 0.015 FJX1 NM_014344 −1.534 0.036 MYH2 NM_017534 −1.524 0.019 ATG4C NM_032852 −1.522 0.034 KCNMB1 NM_004137 −1.520 0.022 CAT NM_001752 −1.517 0.033 ADAM32 NM_145004 −1.516 0.020 PGM5 NM_021965 −1.508 0.004 NOD1 NM_006092 −1.505 0.004 KALRN NM_001024660 −1.497 0.047 FAM106A NR_026809 −1.494 0.033 TTYH2 NM_032646 −1.493 0.044 MFHAS1 NM_004225 −1.488 0.013 GRM7 NM_181874 −1.479 0.019 Bolonna, 2001 - PMID: 11163549 RASL10A NM_001007279 −1.478 0.023 Saito, 2010 - PMID: 20537721 GMPR NM_006877 −1.477 0.024 Lin, 2009 - PMID: 19694819 CRISPLD1 NM_031461 −1.471 0.022 TAS2R4 NM_016944 −1.468 0.009 THUMPD2 NM_025264 −1.467 0.003 LFNG NM_001040167 −1.466 0.013 PPP2R5A NM_006243 −1.466 0.000 LOC162632 NR_003190 −1.466 0.033 URB1 NM_014825 −1.464 0.007 RASA4 NM_006989 −1.462 0.024 FLJ16734 AK131514 −1.461 0.050 C1orf62 NM_152763 −1.453 0.048 GLIPR2 NM_022343 −1.452 0.012 RAB7L1 NM_003929 −1.450 0.025 X IMMP2L NM_032549 −1.448 0.002 IFIT2 NM_001547 −1.447 0.002 NDST3 NM_004784 −1.445 0.014 WASF2 NM_006990 −1.445 0.000 FAM106A NR_026809 −1.445 0.029 SORD NM_003104 −1.444 0.004 B3GALT5 NM_033171 −1.442 0.038 GRHL1 NM_198182 −1.440 0.009 FBXL3 NM_012158 −1.439 0.006 CACNG7 NM_031896 −1.439 0.024 AQP7 NM_001170 −1.436 0.002 QDPR NM_000320 −1.435 0.049 X ABLIM1 NM_002313 −1.433 0.041 TAF1C NM_005679 −1.433 0.005 BAG3 NM_004281 −1.431 0.025 Ikeda, 2009 - PMID: 19850283 RNASEH2B NM_024570 −1.430 0.011 SNORA49 NR_002979 −1.429 0.017 PHF17 NM_199320 −1.427 0.032 C13orf38 NM_001144981 −1.426 0.008 C9orf21 NM_153698 −1.423 0.012 HIST1H4D NM_003539 −1.423 0.009 X FAM106A NR_026809 −1.422 0.023 PBK NM_018492 −1.422 0.041 GNPDA1 NM_005471 −1.420 0.042 X LRRC61 NM_001142928 −1.420 0.018 PRKG1 NM_001098512 −1.417 0.011 F2R NM_001992 −1.416 0.022 RHPN1 NM_052924 −1.416 0.031 RAP2A NM_021033 −1.414 0.007 MST1 NM_020998 −1.413 0.015 DYNC1LI2 NM_006141 −1.413 0.027 X PLCD1 NM_006225 −1.412 0.007 FUT8 NM_178155 −1.412 0.040 SPTAN1 NM_001130438 −1.411 0.033 Murakami, 1999 - PMID: 10402491 FGFR3 NM_000142 −1.409 0.008 Jungerius, 2007 - X PMID: 17893707 PITPNC1 NM_181671 −1.409 0.042 CA13 NM_198584 −1.407 0.031 EZR NM_003379 −1.407 0.029 MGC13005 NR_024005 −1.403 0.015 DCHS2 NM_017639 −1.402 0.018 SLC44A1 NM_080546 −1.401 0.034 DNHD1 NM_173589 −1.400 0.024 C8orf79 NM_020844 −1.396 0.046 TMEM185B NR_000034 −1.395 0.008 SNORA41 NR_002590 −1.395 0.013 CHST15 NM_015892 −1.394 0.024 CCDC144C NR_023380 −1.394 0.026 UBQLN4 NM_020131 −1.394 0.043 SEMA4B NM_020210 −1.393 0.048 C1orf183 NM_019099 −1.393 0.029 NPNT NM_001033047 −1.391 0.001 ARID5A NM_212481 −1.391 0.014 WWP1 NM_007013 −1.386 0.004 PAQR6 NM_024897 −1.385 0.000 REV3L NM_002912 −1.385 0.047 SNORD52 NR_002742 −1.385 0.033 KAT2A NM_021078 −1.380 0.013 X BAI1 NM_001702 −1.378 0.014 TRAF3IP2 NM_147686 −1.377 0.022 CEP78 NM_001098802 −1.377 0.000 EGLN3 NM_022073 −1.375 0.002 FGD3 NM_001083536 −1.372 0.003 MYBL1 NM_001080416 −1.372 0.028 DLEU2 NR_002612 −1.372 0.047 ALDH7A1 NM_001182 −1.371 0.014 X X BLVRA NM_000712 −1.368 0.003 LCAT NM_000229 −1.367 0.001 LCTL NM_207338 −1.367 0.024 FABP4 NM_001442 −1.366 0.008 DOCK7 NM_033407 −1.364 0.021 CDK5RAP2 NM_018249 −1.363 0.014 SOBP NM_018013 −1.362 0.042 SEMA4C NM_017789 −1.362 0.044 MSTP9 NR_002729 −1.362 0.017 C16orf93 NM_001014979 −1.360 0.034 CLN8 NM_018941 −1.359 0.011 METTL7A NM_014033 −1.358 0.045 X CLN8 NM_018941 −1.358 0.028 SGCG NM_000231 −1.357 0.030 ESCO2 NM_001017420 −1.356 0.023 TANC1 NM_033394 −1.356 0.041 SPTB NM_001024858 −1.355 0.013 SEPN1 NM_020451 −1.354 0.047 KIAA1618 NM_020954 −1.354 0.006 ERI1 NM_153332 −1.354 0.029 LOC400464 AK127420 −1.351 0.014 THBS4 NM_003248 −1.348 0.001 RNF213 NM_020914 −1.347 0.029 X SLC35D1 NM_015139 −1.347 0.011 SNRPG NM_003096 −1.346 0.002 GPR37L1 NM_004767 −1.345 0.014 GAL3ST4 NM_024637 −1.343 0.037 FAM53B NM_014661 −1.343 0.035 LSM6 NM_007080 −1.340 0.013 ZFP36L1 NM_004926 −1.339 0.006 MAML2 NM_032427 −1.338 0.031 SNORD109A NR_001295 −1.336 0.037 SNORD109A NR_001295 −1.336 0.037 TM7SF2 NM_003273 −1.333 0.037 X UNQ9370 AY358254 −1.333 0.016 PINK1 NM_032409 −1.331 0.010 Funayama, 2008 - X PMID: 18546294 GPR155 NM_001033045 −1.330 0.031 TST NM_003312 −1.330 0.019 X X X ZNF436 NM_001077195 −1.328 0.031 LRRN2 NM_006338 −1.327 0.048 TCEA3 NM_003196 −1.327 0.049 NHSL1 AK299585 −1.326 0.034 FAM182A NR_026713 −1.323 0.010 ARL6IP6 NM_152522 −1.321 0.035 SCARNA17 NR_003003 −1.317 0.006 NBEA NM_015678 −1.317 0.032 X FAM182A NR_026713 −1.316 0.011 DNHD1 NM_144666 −1.314 0.014 PIK3IP1 NM_052880 −1.314 0.013 FNTB NM_002028 −1.313 0.001 CNN3 NM_001839 −1.313 0.046 CENPQ NM_018132 −1.313 0.022 COQ2 NM_015697 −1.311 0.004 X ADCY7 NM_001114 −1.310 0.005 PSENEN NM_172341 −1.310 0.009 LOC440957 NM_001124767 −1.310 0.035 NACC2 NM_144653 −1.308 0.032 FAM181A BC009073 −1.308 0.022 C14orf149 NM_144581 −1.308 0.028 DAG1 NM_004393 −1.307 0.013 HSD17B3 NM_000197 −1.307 0.002 FLJ00049 AK024457 −1.306 0.007 VASH1 NM_014909 −1.306 0.028 NR2F1 NM_005654 −1.305 0.029 X MAN2A2 NM_006122 −1.305 0.003 X KCNG4 NM_172347 −1.302 0.006 OR2J3 NM_001005216 −1.302 0.042 FAM168A EF363480 −1.301 0.023 X FAM3C NM_014888 −1.301 0.021 SH3KBP1 AY423734 −1.301 0.010 C17orf61 BC030270 −1.300 0.015 ARHGEF17 NM_014786 −1.300 0.039 SLC25A12 NM_003705 1.300 0.026 Hong, 2007 - X PMID: 17693006 KIAA0802 BC040542 1.300 0.018 CPD NM_001304 1.301 0.030 X MKNK2 NM_199054 1.301 0.008 PRICKLE2 NM_198859 1.301 0.006 SESN1 NM_014454 1.304 0.026 X FOXN3 NM_001085471 1.304 0.004 X HIVEP1 NM_002114 1.304 0.000 SLAIN2 NM_020846 1.306 0.005 X KREMEN1 NM_001039570 1.306 0.022 Aleksic, 2010 - PMID: 20153141 ADAMTSL1 NM_001040272 1.306 0.004 PNOC NM_006228 1.307 0.001 Blaveri, 2001 - X PMID: 11436130 WNT3 NM_030753 1.308 0.008 AP2M1 NM_004068 1.310 0.018 ST7 NM_018412 1.311 0.024 FAM35A NM_019054 1.312 0.032 ZNF618 NM_133374 1.312 0.015 FLJ13197 NR_026804 1.313 0.005 X LRP4 NM_002334 1.315 0.046 C9orf125 BC033550 1.317 0.039 FAM35A NM_019054 1.318 0.028 EIF2A NM_032025 1.320 0.005 SBNO1 NM_018183 1.320 0.042 KLF12 NM_007249 1.321 0.039 ZNF124 NM_003431 1.323 0.023 SMYD3 NM_022743 1.323 0.014 X KLHL29 BC015667 1.324 0.001 AKR1C3 NM_003739 1.326 0.036 ZNF217 NM_006526 1.326 0.022 PDE10A NM_006661 1.326 0.033 TCF4 NM_001083962 1.330 0.015 Bowen, 2000 - X X PMID: 10909126 AMOTL2 NM_016201 1.333 0.044 X RHOBTB1 NR_024556 1.333 0.023 POLB NM_002690 1.333 0.038 X ZNF616 NM_178523 1.334 0.045 SEC31A NM_014933 1.335 0.042 X SMC5 NM_015110 1.338 0.034 ADORA2B NM_000676 1.339 0.003 X BOC NM_033254 1.342 0.004 KCTD10 NM_031954 1.344 0.011 X SPRY4 NM_030964 1.347 0.031 Zaharieva, 2008 - PMID: 18298822 NTF3 NM_002527 1.349 0.026 Arinami, 1996 - PMID: 8925252 NUP93 NM_014669 1.356 0.022 CNGA3 NM_001298 1.361 0.023 KLF9 NM_001206 1.361 0.004 AUTS2 NM_015570 1.361 0.007 FARP1 NM_005766 1.363 0.043 P2RX3 NM_002559 1.364 0.024 HS3ST3A1 NM_006042 1.365 0.032 ZNF616 BC032805 1.369 0.038 CNTN2 NM_005076 1.372 0.046 Jungerius, 2007 - PMID: 17893707 SNORD36B NR_000017 1.376 0.016 STK24 NM_003576 1.376 0.007 X UNQ3028 AY358789 1.377 0.010 C17orf75 NM_022344 1.378 0.037 X ZIC5 NM_033132 1.378 0.005 CASP1 NM_033292 1.382 0.004 FAM19A4 NM_182522 1.383 0.034 EIF4B NM_001417 1.385 0.005 AXIN2 NM_004655 1.385 0.019 PDP1 NM_001161778 1.386 0.016 FRMD4A NM_018027 1.386 0.037 SLMO2 NM_016045 1.386 0.017 INADL NM_176877 1.388 0.034 X RPL21 NM_000982 1.389 0.019 X KIRREL3 NM_032531 1.391 0.003 TNFAIP3 NM_006290 1.392 0.009 X GPR137C NM_001099652 1.395 0.041 SCPEP1 NM_021626 1.396 0.011 CRTC3 NM_022769 1.400 0.001 PIK3R3 NM_003629 1.403 0.033 ZNF823 NM_001080493 1.405 0.004 WNT2B NM_024494 1.407 0.031 Proitsi, 2008 - PMID: 17553464 GAS2L3 NM_174942 1.409 0.009 DGKE NM_003647 1.412 0.025 TSC22D2 NM_014779 1.412 0.002 ZNF583 NM_152478 1.414 0.025 ZNF618 NM_133374 1.417 0.009 ATF3 NM_001040619 1.418 0.039 Drexhage, 2010 - PMID: 20633309 MAPK8 NM_002750 1.420 0.044 ATOH8 NM_032827 1.423 0.014 CA11 NM_001217 1.424 0.011 MYT1 NM_004535 1.425 0.036 Jungerius, 2007 - PMID: 17893707 C2CD2 NM_015500 1.427 0.002 SALL4 NM_020436 1.427 0.015 TTC6 BC103915 1.428 0.037 SLC41A2 NM_032148 1.428 0.040 QPCT NM_012413 1.432 0.020 TRIB1 NM_025195 1.433 0.010 TRPS1 NM_014112 1.434 0.005 B3GALT1 NM_020981 1.436 0.037 TIMP2 NM_003255 1.438 0.018 ROBO3 NM_022370 1.441 0.030 FAM107B BC072452 1.442 0.005 X HFM1 NM_001017975 1.444 0.036 STOX2 NM_020225 1.446 0.004 ZNF626 NM_145297 1.461 0.009 LGALS8 NM_006499 1.462 0.039 X ZNF841 NM_001136499 1.463 0.003 DUSP5P NR_002834 1.463 0.026 HSPA1B NM_005346 1.464 0.006 Kim, 2008 - PMID: 18299791 HSPA1B NM_005346 1.464 0.005 Kim, 2008 - PMID: 18299792 HSPA1B NM_005346 1.464 0.005 Kim, 2008 - PMID: 18299793 ZYG11A NM_001004339 1.468 0.023 ZIC2 NM_007129 1.474 0.018 Fallin, 2005 - PMID: 16380905 PTGDS NM_000954 1.475 0.026 Li, 2008 - PMID: 18349703 X PDE4DIP NM_022359 1.475 0.032 X X IFI44 NM_006417 1.480 0.023 RNASEL NM_021133 1.482 0.017 HECTD2 NM_182765 1.486 0.023 ZNF295 NM_001098402 1.491 0.015 C1QTNF6 NM_031910 1.496 0.002 Takahashi, 2003 - PMID: 12815732 XRRA1 NM_182969 1.498 0.001 CACNA2D2 NM_001005505 1.501 0.049 X ADAMTS18 NM_199355 1.507 0.008 JAZF1 NM_175061 1.514 0.033 EPB41 NM_203342 1.517 0.006 X CMIP NM_198390 1.519 0.006 MRAS NM_012219 1.520 0.005 S1PR3 NM_005226 1.521 0.001 SAMD9 NM_017654 1.526 0.036 MYL12A NM_006471 1.528 0.009 FGD6 NM_018351 1.532 0.010 ZNF536 NM_014717 1.533 0.006 MSX2 NM_002449 1.534 0.028 HSPA1A NM_005345 1.534 0.018 Kim, 2008 - PMID: 18299791 DISP1 NM_032890 1.540 0.033 HSPA1A NM_005345 1.540 0.018 Kim, 2008 - PMID: 18299792 BMI1 NM_005180 1.542 0.024 X WT1 NM_024424 1.542 0.010 NOX4 NR_026571 1.543 0.013 LMNA NM_170707 1.557 0.031 X SPOCK3 NM_001040159 1.567 0.046 X X VASH2 NM_024749 1.567 0.017 X MAP3K13 NM_004721 1.570 0.029 X TOX3 NM_001080430 1.574 0.030 C10orf118 NM_018017 1.574 0.002 EDIL3 NM_005711 1.575 0.033 X X CPS1 NM_001875 1.577 0.049 DCT NM_001922 1.579 0.009 ZNF737 NM_001159293 1.581 0.024 DEPDC6 NM_022783 1.588 0.034 CDC42EP3 NM_006449 1.595 0.003 X X SIPA1L2 NM_020808 1.599 0.003 GLRA1 NM_001146040 1.603 0.031 PRSS12 NM_003619 1.605 0.026 BSCL2 NM_001130702 1.606 0.044 FGFR1 NM_023110 1.608 0.001 Jungerius, 2007 - PMID: 17893707 PARP14 NM_017554 1.619 0.050 RHOBTB3 NM_014899 1.625 0.032 X X X DUSP5P AK055963 1.632 0.017 LRRC55 NM_001005210 1.642 0.034 VEGFC NM_005429 1.647 0.022 KIAA1199 NM_018689 1.653 0.026 SFRP2 NM_003013 1.657 0.042 FAM190A NM_001145065 1.668 0.048 CCNG1 NM_004060 1.685 0.001 NRG1 NM_013958 1.691 0.004 Addington, 2006 - PMID: 17033632 ENPP2 NM_006209 1.695 0.041 X X RARB NM_000965 1.697 0.007 ATL3 ENST00000398868 1.697 0.029 CAMK1D NM_153498 1.699 0.012 KRTAP5-2 NM_001004325 1.702 0.026 RBM24 NM_001143942 1.704 0.027 Lin, 2009 - PMID: 19694819 ZFHX3 NM_006885 1.705 0.004 IGFBPL1 NM_001007563 1.708 0.009 LAMA4 NM_001105206 1.716 0.023 ANKRD44 NM_153697 1.717 0.018 MAL NM_002371 1.720 0.048 Jungerius, 2007 - PMID: 17893707 PCDHB2 NM_018936 1.721 0.037 MYOF NM_013451 1.736 0.023 SLAIN1 NM_001040153 1.738 0.037 RBM9 NM_001082578 1.745 0.039 Amagane, 2010 - X X PMID: 20188514 NR4A2 NM_006186 1.748 0.028 Buervenich, 2000 - X X X X PMID: 11121187 RLBP1L1 NM_173519 1.749 0.045 DUSP4 NM_001394 1.750 0.039 CA14 NM_012113 1.755 0.002 ATL3 NM_015459 1.761 0.028 RIMS2 NM_001100117 1.764 0.031 Weidenhofer, 2009 - PMID: 18490030 GCNT4 NM_016591 1.765 0.011 GDF10 NM_004962 1.774 0.012 PLEKHG4B NM_052909 1.777 0.020 LINGO2 NM_152570 1.779 0.018 CYFIP2 NM_001037332 1.790 0.003 DDX60L NM_001012967 1.796 0.032 ADAMTSL1 NM_001040272 1.801 0.043 PHLDA1 NM_007350 1.827 0.027 X NQO1 NM_000903 1.833 0.047 Hori, 2003 - PMID: 12834817 PDE4D NM_001104631 1.843 0.000 Tomppo, 2009 - PMID: 19251251 LNX1 NM_001126328 1.844 0.017 RTL1 NM_001134888 1.849 0.027 GRB10 NM_001001555 1.852 0.005 ZNF423 NM_015069 1.881 0.012 RND3 NM_005168 1.881 0.024 C11orf41 NM_012194 1.885 0.045 NALCN NM_052867 1.894 0.031 Souza, 2010c - PMID: 20674038 SH3BP5 NM_004844 1.897 0.015 STXBP5 NM_001127715 1.900 0.037 STMN4 NM_030795 1.902 0.021 IFITM3 NM_021034 1.906 0.018 X X PPARGC1A NM_013261 1.935 0.030 Christoforou, 2007 - X PMID: 17457313 COL4A2 NM_001846 1.950 0.022 X FLJ41170 AK123165 1.972 0.033 BZW2 NM_001159767 1.987 0.031 GLI3 NM_000168 1.994 0.001 NKAIN2 NM_001040214 1.996 0.014 TLE1 NM_005077 2.000 0.007 SETBP1 NM_015559 2.000 0.010 NET1 NM_001047160 2.013 0.001 TNFRSF11B NM_002546 2.016 0.011 PIP5K1B NM_003558 2.032 0.025 Ikeda, 2009 - PMID: 19850283 ZNF154 NM_001085384 2.036 0.005 CHMP1B NM_020412 2.070 0.012 LEF1 NM_016269 2.071 0.050 GFPT2 NM_005110 2.097 0.010 X ARHGAP18 NM_033515 2.106 0.002 Potkin, 2009 - PMID: 19065146 COL4A1 NM_001845 2.137 0.038 DUSP1 NM_004417 2.145 0.029 X HECW1 NM_015052 2.148 0.016 ANGPT1 NM_001146 2.149 0.005 IFITM2 NM_006435 2.154 0.048 NRP2 NM_201266 2.157 0.008 LRRTM4 NM_024993 2.197 0.041 ZIC4 NM_032153 2.238 0.005 MST131 ENST00000423322 2.269 0.012 NT5E NM_002526 2.276 0.015 CFI NM_000204 2.291 0.035 GNG2 NM_053064 2.330 0.046 SLIT2 NM_004787 2.342 0.019 X PLXNA2 NM_025179 2.376 0.014 Betcheva, 2009 - X PMID: 19158809 EPAS1 NM_001430 2.379 0.038 X SLC16A9 NM_194298 2.379 0.006 TOX NM_014729 2.424 0.007 X SV2C NM_014979 2.437 0.014 X C6orf142 NM_138569 2.448 0.035 EBF1 NM_024007 2.455 0.008 MAMDC2 NM_153267 2.489 0.035 CYP26A1 NM_000783 2.498 0.000 NEFL NM_006158 2.508 0.033 Fallin, 2005 - X PMID: 16380905 LOC151760 ENST00000383686 2.513 0.014 ANK3 NM_020987 2.522 0.026 Athanasiu, 2010 - X PMID: 20185149 FGF14 NM_175929 2.527 0.038 Jungerius, 2007 - PMID: 17893707 PXDNL NM_144651 2.554 0.031 CACNA2D3 NM_018398 2.558 0.003 UNC5C NM_003728 2.564 0.003 Ikeda, 2009 - PMID: 19850283 EFNA5 NM_001962 2.595 0.004 FRAS1 NM_025074 2.623 0.015 DACH1 NM_080759 2.674 0.026 GNAL NM_182978 2.675 0.046 Schwab, 1998 - PMID: 9758604 ECEL1 NM_004826 2.877 0.016 ARHGAP29 NM_004815 2.893 0.002 COL12A1 NM_004370 2.916 0.035 MATN2 NM_002380 2.920 0.001 EBF3 NM_001005463 2.936 0.012 O'Donovan, 2008 - PMID: 18677311 PDE1C NM_005020 2.963 0.041 HS3ST3B1 NM_006041 3.091 0.022 ALPK2 NM_052947 3.124 0.029 THSD7A NM_015204 3.142 0.020 PDE7B NM_018945 3.155 0.011 Amann- Zalcenstein, 2006 - PMID: 16773125 PAPPA NM_002581 3.165 0.016 FAM46A NM_017633 3.188 0.004 FIGN NM_018086 3.202 0.020 DCC NM_005215 3.302 0.027 Speight, 2000 - PMID: 10889538 CNTN3 NM_020872 3.355 0.016 CTSC NM_001814 3.375 0.017 SLFN5 NM_144975 3.405 0.034 ATP8A1 NM_006095 3.528 0.043 MAB21L1 NM_005584 3.567 0.049 NEFM NM_005382 3.676 0.020 Fallin, 2005 - PMID: 16380905 RUNX1T1 NM_175634 3.906 0.012 ASS1 NM_000050 3.975 0.011 FAT4 NM_024582 4.384 0.005 ZMAT4 NM_024645 4.434 0.009 VGLL3 NM_016206 4.557 0.003 IFITM1 NM_003641 4.844 0.028 SNORD113-3 NR_003231 5.036 0.043 SNORD114-3 NR_003195 5.156 0.047 SERPINI1 NM_001122752 5.615 0.005 PAX3 NM_181458 6.139 0.006 Jungerius, 2007 - PMID: 17893707

TABLE 6 GO analysis of microarray data identified significantly affected pathways in SCZD hiPSC neurons. Network Statistically Significant GO Genes Significantly Up, Genes Significantly Down, p-value Objects Pathways Fold Change Fold Change 2.93E−06  21/111 Cytoskeleton Remodeling via WNT2B, 1.41 WNT7A, −1.62 TGF and Wnt WNT3, 1.31 ACTN2, −2.33 AXIN2, 1.39 LEF1, 2.07 TCF4, 1.33 PIK3R3, 1.4 COL4A1, 2.14 COL4A2, 1.95 6.39E−06 13/50 Function of MEF2 ITPR2, −1.72 PRKCA, −2.41 KAT2B, −1.56 1.10E−05 12/45 α6-β4-integrins NRG1, 1.69 EGF, −1.98 PDPK1, 1.26 ERBB3, −1.21 MST1, −1.41 PRKCA, −2.41 ITPR2, −1.72 2.34E−05 10/34 Erk signal transduction GRIN1, 1.16 GRIN2A, −1.72 PTPRR, 1.27 PTPRE, −1.7 PRKCA, −2.41 CAMK1, −1.12 3.91E−05 11/43 Notch signaling pathway HDAC2, 1.29 PSENEN, −1.31 NOTCH1, −1.9 DLL1, −1.92 HEY2, −4.41 KAT2B, −1.56 KAT2A, −1.38 6.48E−05 12/53 Wnt signaling pathway WNT2B, 1.41 WNT7A, −1.62 WNT3, 1.31 LRP5, −1.29 WNT7B, 1.14 AXIN, 1.39, LEF1, 2.07 TCF4, 1.33 6.76E−05 10/38 cAMP signaling pathway GNG2, 2.33 ADCY7, −1.31 PRKAR2A, 1.25 ADCY8, −2.03 PPP3CB, 1.23 PRKCA, −2.41 8.52E−05 15/80 NMDA-dependent GRIN1, 1.16 GRIN2A, −1.72 postsynaptic long-term GRM1, 1.27 ADCY8, −2.03 potentiation PRKAR2A, 1.25 PRKCA, −2.41

TABLE 7 Analysis of microarray data of genes affected by CNVs identified in SCZD patients. Fold- Change Predicted (Affected By Affected Type of CNV Patient vs Expression Genotype Patient CNV CNV location Gene Affected p-value Control) p-value (p < 0.05) Patient 1 deletion chr2: 78551233-78576088 BC024248 3.3E−11 −1.04 0.1062 Patient 1 duplication chr5: 17669005-17706691 none 4.4E−09 na na Patient 1 deletion chr7: 110838909-110985533 IMMP2L 7.2E−48 −1.11 0.0360 X Patient 1 deletion chr8: 3607327-3648499 CSMD1 1.0E−46 −1.31 0.0010 X Patient 1 duplication chr8: 36372115-36392410 none 5.8E−13 na na Patient 1 duplication chr10: 44529265-44679123 AK056518 0.0E+00 nd nd Patient 1 duplication chr12: 89860232-89930609 EPYC 0.0E+00 −1.04 0.1767 Patient 1 duplication chr12: 89860232-89930609 C12Orf12 0.0E+00 −1.06 0.1217 Patient 1 deletion chr18: 40170762-40333519 BC051727 5.1E−110 nd nd Patient 2 deletion chr2: 17083353-17103531 none 3.1E−11 na na Patient 2 duplication chr3: 156964346-156985822 C3orf33 1.7E−07 −1.06 0.1658 Patient 2 deletion chr4: 8408598-8424007 ACOX3 1.1E−20 −1.02 0.0509 Patient 2 deletion chr4: 8408598-8424007 AX746755 1.1E−20 nd nd Patient 2 deletion chr5: 27642965-27665975 none 2.2E−15 na na Patient 2 duplication chr6: 74514699-74534191 CD109 1.1E−16 −1.00 0.9222 Patient 2 deletion chr8: 2126589-2147674 AY156957 1.0E−10 nd nd Patient 2 deletion chr8: 2126589-2147674 AX747124 1.0E−10 nd nd Patient 2 deletion chr8: 3969433-4064034 CSMD1 (Intron) 1.0E−36 −1.04 0.5377 Patient 2 deletion chr8: 18896564-18912764 PSD3 (Intron) 1.7E−07 −1.00 0.9401 Patient 2 duplication chr16: 55217605-55276937 MT1E 7.7E−14 −1.03 0.4904 Patient 2 duplication chr16: 55217605-55276937 MT1M 7.7E−14 −1.01 0.7144 Patient 2 duplication chr16: 55217605-55276937 MTB 7.7E−14 nd nd Patient 2 duplication chr16: 55217605-55276937 MT1A 7.7E−14 −1.04 0.1029 Patient 2 duplication chr16: 55217605-55276937 MT1B 7.7E−14 −1.02 0.1023 Patient 2 duplication chr16: 55217605-55276937 MTM 7.7E−14 nd nd Patient 2 duplication chr16: 55217605-55276937 MT1F 7.7E−14 −1.08 0.0198 Patient 2 duplication chr16: 55217605-55276937 MT1G 7.7E−14 −1.03 0.3647 Patient 2 duplication chr16: 55217605-55276937 MT1H 7.7E−14 −1.04 0.2343 Patient 2 duplication chr16: 55217605-55276937 MT1IP 7.7E−14 −1.02 0.2244 Patient 2 duplication chr16: 55217605-55276937 MTW 7.7E−14 nd nd Patient 2 duplication chr16: 55217605-55276937 MT1X 7.7E−14 −1.08 0.0407 Patient 2 duplication chr19: 34010221-34052245 none 0.0E+00 na na Patient 3 duplication chr1: 119726536-119739044 HAO2 2.2E−16 1.01 0.7481 Patient 3 deletion chr2: 17083353-17103531 none 5.7E−12 na na Patient 3 deletion chr4: 8408598-8422722 ACOX3 6.5E−27 −1.03 0.0112 X Patient 3 deletion chr4: 8408598-8422722 AX746755 6.5E−27 nd nd Patient 3 duplication chr6: 74514699-74532358 CD109 9.7E−10 −1.04 0.4356 Patient 3 deletion chr8: 2126589-2147674 AY156957 9.2E−12 nd nd Patient 3 deletion chr8: 2126589-2147674 AX747124 9.2E−12 nd nd Patient 3 deletion chr8: 18896564-18909227 PSD3 (Intron) 3.0E−08 1.07 0.0006 Patient 3 deletion chr18: 1894094-1974770 none 1.9E−14 na na Patient 3 duplication chr19: 50838214-50889101 EML2 1.1E−16 −1.02 0.3370 Patient 3 duplication chr19: 50838214-50889101 GIPR 1.1E−16 1.05 0.0016 X Patient 3 duplication chr19: 50838214-50889101 SNRPD2 1.1E−16 1.07 0.0001 X Patient 4 duplication chr3: 199196414-199382747 LMLN 3.1E−13 −1.03 0.0161 Patient 4 duplication chr3: 199196414-199382747 LOC348840 3.1E−13 −1.01 0.8604 Patient 4 duplication chr5: 160951572-160965569 GABRB2 1.4E−12 −1.04 0.0000 (5′ Intergenic) Patient 4 duplication chr5: 160951572-160965569 GABRA6 1.4E−12 1.01 0.5703 (5′ Intergenic) Patient 4 duplication chr6: 162538658-162595733 PARK2 0.0E+00 1.01 0.6628 Patient 4 deletion chr7: 151346486-151441286 GALNT5 1.0E−59 1.69 0.0000 Patient 4 deletion chr7: 151346486-151441286 GALNT11 1.0E−59 −1.10 0.0000 X Patient 4 deletion chr8: 15464189-15485502 TUSC3 (Intron) 8.3E−25 −1.01 0.3024 Patient 4 deletion chr10: 84525405-84556365 NRG3 isoform 2 6.9E−24 −1.22 0.0005 X Patient 4 deletion chr10: 96489466-96533096 CYP2C19 4.4E−18 1.04 0.1978 Patient 4 deletion chr11: 18556183-18577561 UEVLD 2.2E−20 −1.13 0.0018 X Patient 4 deletion chr12: 8211354-8666816 ZNF705A 2.1E−40 1.03 0.4175 Patient 4 deletion chr12: 8211354-8666816 FAM90A1 2.1E−40 −1.03 0.0540 Patient 4 deletion chr12: 8211354-8666816 CLEC6A 2.1E−40 1.06 0.1207 Patient 4 deletion chr12: 8211354-8666816 CLEC4D 2.1E−40 −1.02 0.7962 Patient 4 deletion chr12: 8211354-8666816 CLEC4E 2.1E−40 −1.04 0.5424 Patient 4 deletion chr12: 8211354-8666816 AICDA 2.1E−40 1.03 0.0545 Patient 4 deletion chr12: 8211354-8666816 CR611653 2.1E−40 nd nd Patient 4 duplication chr12: 50517243-50577958 ANKRD33 0.0E+00 1.02 0.5990 Patient 4 duplication chr12: 69784529-69797993 TSPAN8 2.9E−12 1.15 0.1061 (3′ Intergenic) Patient 4 duplication chr15: 50782920-50827258 KIAA1370 0.0E+00 −1.06 0.0125 (5′ Intergenic) Patient 4 duplication chr15: 50782920-50827258 ONECUT1 0.0E+00 1.00 0.8738 (3′ Intergenic) Patient 4 duplication chr16: 9803856-9814779 GRIN2A 9.9E−07 −1.16 0.0000 (Intron)* Patient 4 duplication chr17: 9923061-10356441 GAS7 0.0E+00 1.08 0.0137 X Patient 4 duplication chr17: 9923061-10356441 MYH13 0.0E+00 1.02 0.0825 Patient 4 duplication chr17: 9923061-10356441 MYH8 0.0E+00 1.02 0.5058 Patient 4 duplication chr17: 9923061-10356441 MYH4 0.0E+00 1.33 0.0065 X Patient 4 duplication chr17: 9923061-10356441 MYH1 0.0E+00 1.89 0.0000 X Patient 4 deletion chr18: 156081-166915 USP14* 8.3E−07 1.03 0.0299 Patient 4 deletion chr20: 61385006-61408612 ARFGAP1 6.1E−09 −1.02 0.0047 X Patient 4 deletion chr20: 61385006-61408612 COL20A1 6.1E−09 1.16 0.0001 Patient 4 deletion chr20: 61385006-61408612 KIAA1510 6.1E−09 nd nd

TABLE 8 Expression analysis of top Affymetrix transcripts misexpressed at well-characterized SCZD CNVs Fold-Change Transcript p-value (SCZD vs ID Cytoband Gene Symbol (Diagnosis) Control) 7919168 1q21.1 PDE4DIP 0.03176 1.48 7919243 1q21.1 CD160 0.06112 1.10 7904907 1q21.1 BCL9 0.06162 1.16 7919226 1q21.1 POLR3C 0.06511 1.17 7919195 1q21.1 0.06621 −1.08 7904883 1q21.1 CHD1L 0.06630 −1.22 7904480 1q21.1 0.06819 −1.24 7904963 1q21.1 0.06819 −1.24 7919193 1q21.1 NUDT4P1 0.02777 −1.27 7919299 1q21.1 LOC100130236 0.09582 −1.10 7981775 15q11.2 DKFZP547L112 0.01185 −1.19 7981781 15q11.2 OR4M2 0.03283 −1.23 7986685 15q11.2 DEXI 0.04303 −1.12 7986601 15q11.2 LOC440243 0.04308 1.12 7981773 15q11.2 0.05008 −1.15 7981752 15q11.2 GOLGA8D 0.11046 −1.11 7981785 15q11.2 OR4N3P 0.11468 1.11 7986563 15q11.2 LOC646057 0.11968 −1.14 7981824 15q11.2 CYFIP1 0.13054 −1.14 7986603 15q11.2 LOC646214 0.16966 1.09 7986820 15q13.1 0.09880 −1.07 7982102 15q13.1 GABRA5 0.15919 1.18 7982127 15q13.1 0.53415 −1.03 7986789 15q13.1 ATP10A 0.53850 1.09 7986822 15q13.1 GABRB3 0.70732 −1.08 7982117 15q13.1 GABRG3 0.84759 −1.07 7982100 15q13.1 0.91167 −1.01 7986836 15q13.1 0.93823 1.00 7982131 15q13.2 GOLGA8G 0.07137 −1.12 7986922 15q13.2 GOLGA8G 0.07137 −1.12 7991695 15q13.2 GOLGA8D 0.14069 −1.11 7986947 15q13.2 GOLGA9P 0.28404 −1.13 7986863 15q13.2 HERC2 0.41947 1.05 7982129 15q13.2 RPL41 0.50117 1.07 7986945 15q13.2 0.61305 −1.06 7982152 15q13.2 0.62512 −1.03 7986943 15q13.2 0.62512 −1.03 7982154 15q13.2 HERC2P2 0.78350 1.03 7986838 15q13.2 OCA2 0.80749 −1.05 7987048 15q13.3 MTMR10 0.03792 −1.27 7982299 15q13.3 LOC390561 0.03795 −1.28 7982185 15q13.3 DEXI 0.04303 −1.12 7982252 15q13.3 DKFZP434L187 0.12698 1.28 7982254 15q13.3 0.16920 1.37 7982230 15q13.3 GOLGA9P 0.21265 −1.14 7982271 15q13.3 GOLGA9P 0.21375 −1.16 7987097 15q13.3 0.24477 −1.08 7986960 15q13.3 FAM189A1 0.28169 −1.10 7982204 15q13.3 HMGN2 0.31280 1.07 7982290 15q13.3 0.32056 −1.24 7987012 15q13.3 CHRFAM7A 0.35454 1.13 7995320 16p11.1 0.00256 −1.13 7995348 16p11.1 0.02650 −1.12 7995338 16p11.1 0.07405 −1.06 7995322 16p11.1 0.08523 −1.11 8001111 16p11.1 UBE2MP1 0.17026 1.16 7995336 16p11.1 0.18118 −1.11 7995324 16p11.1 0.19448 −1.10 7995330 16p11.1 0.19978 −1.14 7995334 16p11.1 0.21771 −1.06 7995326 16p11.1 0.26439 −1.09 7995206 16p11.2 TGFB1I1 0.00371 −1.28 7995007 16p11.2 HSD3B7 0.02001 −1.16 7995292 16p11.2 SLC6A8 0.02141 −1.10 7994541 16p11.2 LAT 0.02255 −1.10 8000932 16p11.2 C16orf93 0.03374 −1.36 8000582 16p11.2 SULT1A2 0.03606 −1.25 7994371 16p11.2 NPIPL3 0.03871 −1.12 8000791 16p11.2 YPEL3 0.04007 −1.20 8000748 16p11.2 HIRIP3 0.04325 −1.12 8003583 16p11.2 KIF22 0.04398 −1.11 7994620 16p11.2 KIF22 0.04517 −1.11 8071206 22q11.21 MRPL40 0.00560 −1.21 8074194 22q11.21 OR11H1 0.00893 −1.06 8074591 22q11.21 RIMBP3B 0.01867 −1.17 8071212 22q11.21 CDC45L 0.03503 −1.20 8071368 22q11.21 TMEM191A 0.04611 1.15 8074204 22q11.21 XKR3 0.04841 1.04 8074569 22q11.21 GGT3P 0.05390 −1.08 8071063 22q11.21 psiTPTE22 0.06227 −1.16 8071259 22q11.21 SEPT5 0.06754 1.24 8074316 22q11.21 GGT3P 0.07437 −1.10 8074890 22q11.23 0.00112 −1.16 8071768 22q11.23 SMARCB1 0.01106 1.08 8074769 22q11.23 RIMBP3C 0.02656 −1.13 8074958 22q11.23 0.09232 1.06 8071545 22q11.23 0.10165 −1.05 8071564 22q11.23 0.11648 −1.15 8074867 22q11.23 POM121L1P 0.12617 1.05 8071737 22q11.23 MIF 0.14101 −1.26 8071676 22q11.23 RAB36 0.14176 −1.25 8074748 22q11.23 PI4KAP2 0.14569 −1.21 8074931 22q11.23 ZNF70 0.16735 1.06

TABLE 9 Analysis of inheritance of CNVs identified in SCZD patient 4. Relation to CNV Proband Type of CNV CNV location p-value Father deletion chr2: 6684377-6870214 3.87E−85 Patient 5 deletion chr2: 6683379-6870214 2.23E−119 Patient 5 deletion chr3: 128418717-128432973 8.82E−32 Mother duplication chr3: 199195203-199367408 7.86E−08 Patient 4 duplication chr3: 199196414-199376895 1.18E−11 Father duplication chr6: 162541018-162595733 3.59E−13 Patient 4 duplication chr6: 162541018-162595733 1.98E−13 Patient 5 duplication chr6: 162541018-162595733 2.22E−16 Patient 5 deletion chr6: 170195821-170206320 4.81E−12 Father deletion chr7: 111514132-111536768 1.66E−37 Father deletion chr7: 151348062-151439868 7.98E−39 Patient 4 deletion chr7: 151350927-151437530 7.98E−37 Patient 5 deletion chr7: 151350927-151439868 1.47E−55 Father deletion chr8: 18891576-18910636 7.79E−07 Patient 4 deletion chr8: 15456201-15484626 9.45E−10 Mother duplication chr10: 30514430-30526183 4.68E−10 Patient 4 deletion chr10: 84521261-84556365 5.26E−16 Patient 5 deletion chr10: 84522764-84556365 1.62E−28 Patient 4 deletion chr10: 96489466-96535919 3.39E−08 Patient 5 deletion chr10: 96489466-96554411 3.23E−11 Father deletion chr11: 18563533-18577561 4.79E−07 Patient 4 deletion chr11: 18562081-18579036 7.72E−08 Patient 5 deletion chr11: 18563533-18577561 4.84E−13 Father deletion chr12: 8493239-8667968 1.26E−34 Patient 4 deletion chr12: 8493239-8673506 1.64E−38 Mother duplication chr12: 50517243-50578630 2.55E−15 Patient 4 duplication chr12: 50517243-50577958 2.44E−15 Patient 5 duplication chr12: 50517243-50577958 0.00E+00 Father duplication chr12: 50975625-51067874 1.68E−14 Father duplication chr12: 69784529-69797993 7.13E−08 Patient 4 duplication chr12: 69785475-69805349 5.45E−08 Patient 4 duplication chr15: 50782920-50827258 0.00E+00 Father duplication chr17: 9929175-10356441 0.00E+00 Patient 4 duplication chr17: 9929175-10356441 0.00E+00

TABLE 10 qPCR primers Gene Forward Reverse GAPDH TGTTGCCATCAATGACCCCTT CTCCACGACGTACTCAGCG Actin AAACTGGAACGGTGAAGGTG AGAGAAGTGGGGTGGCTTTT βIII-tubulin ACCTCAACCACCTGGTATCG TTCTTGGCATCGAACATCTG GRIK1 AAAGGTTACGGAGTGGGAAC TCTTTGTTGTCTTCCTCGGG GRIN2A CTTGCTTCAGTTTGTGGGTG AGCCAGCATGTAGAATACGC GRM1 AGCTTGTGACTTGGGATGG TCGATGTTGCTCCACTCAAG GRM7 CCCGAGAATTTTAACGAAGCC ATGGAGATTGTAAGCGTGGTAG ADCY7 CACTCCTTCAACTCCTTCCG TCTCCAGTGCTTTCCATTCG ADCY8 TGCTGACTTCGATGAGTTGC ATGTCCCCACTTGTCTTCAC PDE3A GCGATGAGTCAGGAGATACTG AGAGGTGCTGAGTTATTTGGC PDE4D AGATAAGCCCCATGTGTGAC CCTCCAAAGTGTCCAAAATATCC PDE4DIP CAGAAGGAGAGCATGGAACAG ATGGTTCCTGGAAGGCAAG PDE7B TGCAATCCTTGTAGAATCTGGG ACTAGGGATGGAATCTTTCTGTTG PDE8A GCATCCCCAAATCCCAAATC TCATTTCGTCCAGTCCTTTCC PDE10A GAATTCTGGGCTGAGGGTG GGGTAAGGGTTGTATAGCAGG PRKCA CACCATTCAAGCCCAAAGTG CATACGAGAACCCTTCAAAATCAG RAP2A GGCTTCATCCTCGTCTACAG TCACTTTCCAGGTCCACTTTG RAP1A AGTGTATGCTCGAAATCCTGG AACGTGGACTGAGCTGTAATAG WNT7A AAGGTCTTTGTGGATGCCC GCACTTACATTCCAGCTTCATG LRP5 CACTGCGAGACCGTACAG GTCCGAGTTCAAATCCAGGTAG AXIN2 CAGAGGGACAGGAATCATTCG AACCAACTCACTGGCCTG TCF4 GAACCTGCAAGACACGAAATC CTTCTCACGCTCTGCCTTC LEF1 CATATGCAGCTTTATCCAGGC CACCATGTTTCAGATGTAGGC DISC1 ACTCACCTCATCCCCTCTC CACACTTTTCTCCAAGTTCTG NRG1 ACAAGGCACACAGATCCAAA AAGGCCAAGGGGTCTTAGAG NRG2 CAGAAGAGGGTCCTGACCAT GAGGTGGTTGTGCATCTGCT NRG3 AAAGGACCTGGTGGGCTATT AGAATTCGGATCTGCTCCTG ERBB4 GGAGTATGTCCACGAGCACAA TCGAGTCGTCTTTCTTCCAG PSD-95 ACAAGCGGATCACAGAGGAG CAGATGTAGGGGCCTGAGAG PSD-93 AGCCTGTTACAAGGCAGGAA GCCATCCACCTCGTAGTCTC CYP2C19 AAACGGATTTGTGTGGGAGA ATAGAAGGGCGGGACAGAAG GABRA6 AAGGCTATGACAATCGGCTGC TCAGTCCAGGTCTGGCGGAAA GABRB2 TGCCTGCATGATGGACCTAA TCCTGTTACTGCATTATCAT Lentiviral OCT4 CCCCTGTCTCTGTCACCACT CCACATAGCGTAAAAGGAGCA Lentiviral SOX2 ACACTGCCCCTCTCACACAT CATAGCGTAAAAGGAGCAACA Lentiviral cMYC AAGAGGACTTGTTGCGGAAA TTGTAATCCAGAGGTTGATTATCG Lentiviral KLF4 GACCACCTCGCCTTACACAT CATAGCGTAAAAGGAGCAACA Endogenous OCT4 TGTACTCCTCGGTCCCTTTC TCCAGGTTTTCTTTCCCTAGC Endogenous SOX2 GCTAGTCTCCAAGCGACGAA GCAAGAAGCCTCTCCTTGAA Endogenous cMYC CGGAACTCTTGTGCGTAAGG CTCAGCCAAGGTTGTGAGGT Endogenous KLF4 TATGACCCACACTGCCAGAA TGGGAACTTGACCATGATTG NANOG CAGTCTGGACACTGGCTGAA CTCGCTGATTAGGCTCCAAC TDGF1 (CRIPTO) AAGATGGCCCGCTTCTCTTAC AGATGGACGAGCAAATTCCTG ZFP42 (REX1) AACGGGCAAAGACAAGACAC GCTGACAGGTTCTATTTCCGC 

1. A method of determining whether a test compound is capable of improving a schizophrenia marker function in a hiPSC-derived neural cell, said method comprising: (i) contacting a test compound with a hiPSC-derived neural cell, wherein said hiPSC-derived neural cell is derived from a schizophrenic subject, and wherein said hiPSC-derived neural cell exhibits a schizophrenia marker function at a first level in the absence of said test compound; (ii) after step (i), determining a second level of said schizophrenia marker function; and (iii) comparing the second level to a control level, wherein a smaller difference between the second level and the control level than between the first level and the control level indicates said test compound is capable of improving said schizophrenia marker function.
 2. The method of claim 1, wherein said smaller difference indicates said schizophrenic subject is responsive to said test compound.
 3. The method of claim 2, further comprising administering an effective amount of said test compound to said schizophrenic subject in need of treatment for schizophrenia.
 4. The method of claim 1, wherein said hiPSC-derived neural cell is made by a method comprising: (i) reprogramming a fibroblast cell thereby forming a fibroblast-derived hiPSC; and (ii) differentiating said fibroblast-derived hiPSC thereby forming said hiPSC-derived neural cell.
 5. The method of claim 4, wherein said fibroblast cell is obtained from a schizophrenic subject.
 6. The method of claim 1, wherein said schizophrenia marker function is: a number of neurites extending from said hiPSC-derived neural cell, a level of PSD95 expressed by said hiPSC-derived neural cell, a level of synaptic density of said hiPSC-derived neural cell, a level of neural connectivity of said hiPSC-derived neural cell, a level of synaptic plasticity of said hiPSC-derived neural cell, a level of NRG1 expressed by said hiPSC-derived neural cell, a level of a glutamate receptor expressed by said hiPSC-derived neural cell, a level of a neuregulin pathway component expressed by said hiPSC-derived neural cell, a level of a synaptic protein expressed by said hiPSC-derived neural cell, a level of a cAMP component expressed by said hiPSC-derived neural cell, a level of a calcium signaling pathway component expressed by said hiPSC-derived neural cell, a level of a Wnt signaling pathway component expressed by said hiPSC-derived neural cell, a level of a Notch growth factor expressed by said hiPSC-derived neural cell, a level of neural migration of said hiPSC-derived neural cell, or a level of a cell adhesion component expressed by said hiPSC-derived neural cell.
 7. A method of determining whether a subject is schizophrenic, said method comprising: (i) determining a level of a schizophrenia marker function in a hiPSC-derived neural cell derived from a subject; (ii) comparing said level to a control level, wherein a difference between said level and said control level indicates said subject is schizophrenic.
 8. The method of claim 7, further comprising: (iii) quantitating said difference thereby determining a test quantity, and (iv) comparing said test quantity to a control quantity thereby determining a severity of said subject's schizophrenia.
 9. The method of claim 7, further comprising, prior to step (i): (a) obtaining a cell from said subject; (b) reprogramming said cell thereby forming a hiPSC; (c) allowing said hiPSC to differentiate thereby forming a hiPSC-derived neural cell derived from said subject.
 10. The method of claim 9, wherein said cell is a fibroblast cell.
 11. The method of claim 9, further comprising treating said subject in need of treatment for schizophrenia.
 12. A method of identifying a schizophrenia marker function, said method comprising: (i) obtaining a cell from a schizophrenic subject; (ii) reprogramming said cell thereby forming a hiPSC; (iii) allowing said hiPSC to differentiate thereby forming a hiPSC-derived neural cell derived from said schizophrenic subject; and (iv) determining a level of a function of said hiPSC-derived neural cell and comparing said level to a control level, wherein a difference between said level and said control level indicates said function is a schizophrenia marker function.
 13. The method of claim 12, wherein said cell is a fibroblast cell.
 14. A method of determining whether a schizophrenic subject is responsive to treatment with a loxapine compound, said method comprising: (i) contacting a loxapine compound with a hiPSC-derived neural cell, wherein said hiPSC-derived neural cell is derived from said schizophrenic subject, and wherein said hiPSC-derived neural cell exhibits a loxapine marker function at a first level in the absence of loxapine; (ii) after step (i), determining a second level of said loxapine marker function; and (iii) comparing the second level to a control level, wherein a smaller difference between the second level and the control level than between the first level and the control level indicates said schizophrenic subject is responsive to treatment with a loxapine compound.
 15. The method of claim 14, further comprising administering an effective amount of a loxapine compound to said schizophrenic subject in need of treatment for schizophrenia.
 16. The method of claim 14, wherein said hiPSC-derived neural cell is made by a method comprising: (i) reprogramming a fibroblast cell thereby forming a fibroblast-derived hiPSC; and (ii) differentiating said fibroblast-derived hiPSC thereby forming said hiPSC-derived neural cell.
 17. The method of claim 14, wherein said loxapine marker function is: a level of a cytoskeleton remodeling component expressed by said hiPSC-derived neural cell, a level of TGF signaling pathway component expressed by said hiPSC-derived neural cell, a level of NRG1 expressed by said hiPSC-derived neural cell, a level of a glutamate receptor expressed by said hiPSC-derived neural cell, a level of neural connectivity of said hiPSC-derived neural cell, or a level of a cell adhesion component expressed by said hiPSC-derived neural cell.
 18. The method of claim 14, wherein said loxapine marker function is: a level of a cytoskeleton remodeling component expressed by said hiPSC-derived neural cell, a level of a TGF signaling pathway component expressed by said hiPSC-derived neural cell, a level of NRG1 expressed by said hiPSC-derived neural cell, a level of a glutamate receptor expressed by said hiPSC-derived neural cell, a level of neural connectivity of said hiPSC-derived neural cell, and a level of a cell adhesion component expressed by said hiPSC-derived neural cell.
 19. A method of determining whether a test compound is capable of improving a loxapine marker function, said method comprising: (i) contacting a test compound with a hiPSC-derived neural cell, wherein said hiPSC-derived neural cell is derived from a schizophrenic subject, and wherein said hiPSC-derived neural cell exhibits a loxapine marker function at a first level in the absence of said test compound; (ii) after step (i), determining a second level of said loxapine marker function; and (iii) comparing the second level to a control level, wherein a smaller difference between the second level and the control level than between the first level and the control level indicates said test compound is capable of improving said loxapine marker function.
 20. The method of claim 19, wherein said smaller difference indicates said schizophrenic subject is responsive to said test compound.
 21. The method of claim 20, further comprising administering an effective amount of said test compound to said schizophrenic subject in need of treatment for schizophrenia.
 22. The method of claim 19, wherein said hiPSC-derived neural cell is made by a method comprising: (i) reprogramming a fibroblast cell thereby forming a fibroblast-derived hiPSC; and (ii) differentiating said fibroblast-derived hiPSC thereby forming said hiPSC-derived neural cell.
 23. The method of claim 22, wherein said fibroblast cell is obtained from a schizophrenic subject.
 24. The method of claim 19, wherein said loxapine marker function is: a level of a cytoskeleton remodeling component expressed by said hiPSC-derived neural cell, a level of TGF signaling pathway component expressed by said hiPSC-derived neural cell, a level of NRG1 expressed by said hiPSC-derived neural cell, a level of a glutamate receptor expressed by said hiPSC-derived neural cell, a level of neural connectivity of said hiPSC-derived neural cell, or a level of a cell adhesion component expressed by said hiPSC-derived neural cell. 